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Wei G, Chen Y, Wang J, Feng L. Molecular cloning and characterization of farnesyl diphosphate synthase from Rosa rugosa Thunb associated with salinity stress. PeerJ 2024; 12:e16929. [PMID: 38435988 PMCID: PMC10909355 DOI: 10.7717/peerj.16929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
Rosa rugosa, a renowned ornamental plant, is cultivated for its essential oil containing valuable monoterpenes, sesquiterpenes, and other compounds widely used in the floriculture industry. Farnesyl diphosphate synthase (FPPS) is a key enzyme involved in the biosynthesis of sesquiterpenes and triterpenes for abiotic or biotic stress. In this study, we successfully cloned and characterized a full-length FPPS- encoding cDNA identified as RrFPPS1 using RT-PCR from R. rugosa. Phylogenetic analysis showed that RrFPPS1 belonged to the angiosperm-FPPS clade. Transcriptomic and RT-qPCR analyses revealed that the RrFPPS1 gene had tissue-specific expression patterns. Subcellular localization analysis using Nicotiana benthamiana leaves showed that RrFPPS1 was a cytoplasmic protein. In vitro enzymatic assays combined with GC-MS analysis showed that RrFPPS1 produced farnesyl diphosphate (FPP) using isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates to provide a precursor for sesquiterpene and triterpene biosynthesis in the plant. Additionally, our research found that RrFPPS1 was upregulated under salt treatment. These substantial findings contribute to an improved understanding of terpene biosynthesis in R. rugosa and open new opportunities for advancements in horticultural practices and fragrance industries by overexpression of the RrFPPS1 gene in vivo increased FPP production and subsequently led to elevated sesquiterpene yields in the future. The knowledge gained from this study can potentially lead to the development of enhanced varieties of R. rugosa with improved aroma, medicinal properties, and resilience to environmental stressors.
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Affiliation(s)
- Guo Wei
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Yudie Chen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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2
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Satta A, Esquirol L, Ebert BE, Newman J, Peat TS, Plan M, Schenk G, Vickers CE. Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase. FEBS J 2022; 289:6672-6693. [PMID: 35704353 PMCID: PMC9796789 DOI: 10.1111/febs.16556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/03/2022] [Accepted: 06/14/2022] [Indexed: 01/07/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short-chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC 7942 and Synechocystis sp. PCC 6803. Each species has a single putative SPT (SeCrtE and SyCrtE, respectively). Sequence analysis identified these as type-II geranylgeranyl pyrophosphate synthases (GGPPSs) with high homology to GGPPSs found in the plastids of green plants and other photosynthetic organisms. In vitro analysis demonstrated that SyCrtE is multifunctional, producing geranylgeranyl pyrophosphate (GGPP; C20 ) primarily but also significant amounts of farnesyl pyrophosphate (FPP, C15 ) and geranyl pyrophosphate (GPP, C10 ); whereas SeCrtE appears to produce only GGPP. The crystal structures were solved to 2.02 and 1.37 Å, respectively, and the superposition of the structures against the GGPPS of Synechococcus elongatus sp. PCC 7002 yield a root mean square deviation of 0.8 Å (SeCrtE) and 1.1 Å (SyCrtE). We also discovered that SeCrtE is co-encoded in an operon with a functional GGPP phosphatase, suggesting metabolic pairing of these two activities and a putative function in tocopherol biosynthesis. This work sheds light on the activity of SPTs and terpenoid synthesis in cyanobacteria. Understanding native prenyl phosphate metabolism is an important step in developing approaches to engineering the production of different chain-length terpenoids in cyanobacteria.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Janet Newman
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Thomas S. Peat
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Manuel Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaAustralia,Sustainable Minerals InstituteThe University of QueenslandSt. LuciaAustralia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia,Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia,ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneAustralia
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3
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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.
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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.
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Zhang C, Liu H, Zong Y, Tu Z, Li H. Isolation, expression, and functional analysis of the geranylgeranyl pyrophosphate synthase (GGPPS) gene from Liriodendron tulipifera. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:700-711. [PMID: 34214780 DOI: 10.1016/j.plaphy.2021.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/08/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Terpenoids are important secondary metabolites in plants and are involved in stress responses and pollinator attraction. Geranylgeranyl pyrophosphate synthase (GGPPS) is a key synthase in the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway of terpenoid synthesis, catalyzing the synthesis of diterpenoids. Liriodendron tulipifera is a nectar plant in North America. Little is known about the key genes involved in the biosynthetic pathways of terpenoids, the precursors of most compounds related to nectar, fragrance and coloring in flowers in L. tulipifera. In this study, the LtuGGPPS2 gene and its promoter (LtuGGPPS2-pro) were cloned from L. tulipifera. The results of sequence alignment showed that the LtuGGPPS2 gene is highly homologous to GGPPS genes of other plants. Subcellular localization analysis showed that the LtuGGPPS2 protein localizes to chloroplasts, suggesting that the LtuGGPPS2 gene is probably related to carotenoid and chlorophyll synthesis. Based on tissue expression profiles revealed by RT-qPCR, the expression level of the LtuGGPPS2 gene was highest in petals. These results were consistent with the changes in volatile and nonvolatile terpenoids in the flowers of L. tulipifera. GUS staining to examine the LtuGGPPS2 promoter indicated that it is responsive to hormones. Overexpression of the LtuGGPPS2 gene increased the carotenoid content and GGPPS enzyme activity in Arabidopsis thaliana, indicating that LtuGGPPS2 is the key terpenoid synthase in the flowers of L. tulipifera. Our findings lay a foundation for further functional analysis of the LtuGGPPS2 gene and deeper investigation of the terpenoid biosynthetic pathway in L. tulipifera.
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Affiliation(s)
- ChengGe Zhang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - HuanHuan Liu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - YaXian Zong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - ZhongHua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - HuoGen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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5
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Maheshwari S, Kim YS, Aripirala S, Murphy M, Amzel LM, Gabelli SB. Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase. Biochemistry 2020; 59:2751-2759. [PMID: 32584028 PMCID: PMC8049779 DOI: 10.1021/acs.biochem.0c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Farnesyl diphosphate synthase (FPPS) is an isoprenoid chain elongation enzyme that catalyzes the sequential condensation of dimethylallyl diphosphate (C5) with isopentenyl diphosphate (IPP; C5) and the resulting geranyl diphosphate (GPP; C10) with another molecule of IPP, eventually producing farnesyl diphosphate (FPP; C15), which is a precursor for the biosynthesis of a vast majority of isoprenoids. Previous studies of FPPS have highlighted the importance of the structure around the hydrophobic chain elongation path in determining product specificity. To investigate what structural features define the final chain length of the product in FPPS from Leishmania major, we designed and expressed six mutants of LmFPPS by replacing small amino acids around the binding pocket with bulky residues. Using enzymatic assays, binding kinetics, and crystallographic studies, we analyzed the effects of these mutations on the activity and product specificity of FPPS. Our results revealed that replacement of Thr-164 with tryptophan and phenylalanine completely abolished the activity of FPPS. Intriguingly, the T164Y substitution displayed dual product specificity and produced a mixture GPP and FPP as final products, with an activity for FPP synthesis that was lower than that of the wild-type enzyme. These data indicate that Thr-164 is a potential regulator of product specificity.
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Affiliation(s)
- Sweta Maheshwari
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yu Seon Kim
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Srinivas Aripirala
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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6
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A Simple In Vitro Assay to Measure the Activity of Geranylgeranyl Diphosphate Synthase and Other Short-Chain Prenyltransferases. Methods Mol Biol 2019; 2083:27-38. [PMID: 31745910 DOI: 10.1007/978-1-4939-9952-1_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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7
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Kim S, Kim EJ, Park JB, Kim SW, Kim KJ. Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6. Biochem Biophys Res Commun 2019; 518:479-485. [PMID: 31427080 DOI: 10.1016/j.bbrc.2019.08.071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 10/26/2022]
Abstract
Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 α-helices (α1-α15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.
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Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea
| | - Eun-Jung Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Ji-Bin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea.
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8
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Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC, Villanueva L, Wienk H, Sinninghe Damsté JS. New Insights Into the Polar Lipid Composition of Extremely Halo(alkali)philic Euryarchaea From Hypersaline Lakes. Front Microbiol 2019; 10:377. [PMID: 30930858 PMCID: PMC6423904 DOI: 10.3389/fmicb.2019.00377] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
We analyzed the polar membrane lipids of 13 strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations, and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2, and (d) novel cardiolipins containing a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the 13 strains could be generally separated into two groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glycerol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the 13 strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.
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Affiliation(s)
- Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Wang J, Lin HX, Su P, Chen T, Guo J, Gao W, Huang LQ. Molecular cloning and functional characterization of multiple geranylgeranyl pyrophosphate synthases (ApGGPPS) from Andrographis paniculata. PLANT CELL REPORTS 2019; 38:117-128. [PMID: 30448883 DOI: 10.1007/s00299-018-2353-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/07/2018] [Indexed: 05/19/2023]
Abstract
We found that ApGGPPS1, ApGGPPS2, and ApGGPPS3 can convert IPP and DMAPP to GGPP. ApGGPPS2 is probably involved in andrographolide biosynthesis. ApGGPPS3 may be responsible for the synthesis of the cytosolic GGPP. Andrographis paniculata is a traditional herb for the treatment of sore throat, flu, upper respiratory tract infections and other disorders. In A. paniculata, GGPP is not only the precursor of andrographolide and its primary bioactive compounds, but also the precursor of chlorophylls, carotenoids, gibberellins, and abscisic acid, which are the biomolecules of photosynthesis, growth regulation and other physiological and ecological processes. In this study, four cDNAs (named ApGGPPS1, ApGGPPS2, ApGGPPS3 and ApGGPPS4) encoding geranylgeranyl pyrophosphate synthases from A. paniculata were putatively isolated. Bioinformatic and phylogenetic analyses suggested that these ApGGPPS are highly similar to the geranylgeranyl pyrophosphate synthases in other plants. Prokaryotic expression showed that ApGGPPS1, ApGGPPS2 and ApGGPPS3 could convert IPP and DMAPP to GGPP, although ApGGPPS4 lacks a similar function. The expression of ApGGPPS2 was similar as ApCPS2 under MeJA treatment, ApCPS2 involved in the biosynthesis pathway of andrographolide (Shen et al., Biotechnol Lett 38:131-137, 2016a), has been proven through Virus-induced Gene Siliencing (VIGS) (Shen et al., Acta Bot Boreal 36:17-22, 2016b), and the subcellular localization of ApGGPPS2 was shown to localize in the plastid, suggested that ApGGPPS2 could be the key synthase in the biosynthesis pathway of andrographolide. In addition, ApGGPPS3 was shown to localize in the cytoplasm, suggested that ApGGPPS3 may be responsible for the synthesis of cytosolic GGPP, which may participate in the synthesis of cytosolic oligoprenols as side chains to produce ubiquinone, dolichols or other isoprenoids, in the synthesis of polyisoprenoids, and in protein prenylation.
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Affiliation(s)
- Jian Wang
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, 100016, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Hui-Xin Lin
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Ping Su
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Tong Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wei Gao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China.
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.
| | - Lu-Qi Huang
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, 100016, China.
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China.
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.
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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.
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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
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11
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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.
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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
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12
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Picard MÈ, Nisole A, Béliveau C, Sen S, Barbar A, Shi R, Cusson M. Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 92:84-92. [PMID: 29183817 DOI: 10.1016/j.ibmb.2017.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is an enzyme from the class of short chain (E)-prenyltransferases that catalyzes the condensation of two molecules of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) to generate the C15 product FPP. In insects, FPPS plays a key role in the biosynthesis of the morphogenetic and gonadotropic "juvenile hormone" (JH). Lepidopteran genomes encode two very distinct FPPS paralogs, one of which ("type-II") is expressed almost exclusively in the JH-producing glands, the corpora allata. This paralog has been hypothesized to display structural features that enable the binding of the bulkier precursors required for the biosynthesis of lepidopteran ethyl-branched JHs. Here, we report on the first crystal structures of an insect FPPS solved to date. Apo, ligand-bound, and inhibitor-bound structures of type-II FPPS (FPPS2) from the spruce budworm, Choristoneura fumiferana (Order: Lepidoptera), were obtained. Comparison of apo and inhibitor-bound enzymes revealed differences in both inhibitor binding and structural plasticity of CfFPPS2 compared to other FPPSs. Our data showed that IPP is not essential to the closure of the C-terminal tail. Ortho-substituted pyridinium bisphosphonates, previously shown to inhibit CfFPPS2, bound to the allylic site, as predicted; however, their alkyl groups were oriented towards the homoallylic binding site, with the bulkier propyl-substituted inhibitor penetrating deeply into the IPP binding pocket. The current study sheds light on the structural basis of substrate specificity of type-II FPPS of the spruce budworm. Through a comparison with other inhibitor-bound FPPSs, we propose several approaches to improve inhibitor selectivity and potency.
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Affiliation(s)
- Marie-Ève Picard
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Audrey Nisole
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Catherine Béliveau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Stephanie Sen
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ, 08628, USA.
| | - Aline Barbar
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Rong Shi
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Michel Cusson
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
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13
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A recruiting protein of geranylgeranyl diphosphate synthase controls metabolic flux toward chlorophyll biosynthesis in rice. Proc Natl Acad Sci U S A 2017; 114:6866-6871. [PMID: 28607067 DOI: 10.1073/pnas.1705689114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plants, geranylgeranyl diphosphate (GGPP) is produced by plastidic GGPP synthase (GGPPS) and serves as a precursor for vital metabolic branches, including chlorophyll, carotenoid, and gibberellin biosynthesis. However, molecular mechanisms regulating GGPP allocation among these biosynthetic pathways localized in the same subcellular compartment are largely unknown. We found that rice contains only one functionally active GGPPS, OsGGPPS1, in chloroplasts. A functionally active homodimeric enzyme composed of two OsGGPPS1 subunits is located in the stroma. In thylakoid membranes, however, the GGPPS activity resides in a heterodimeric enzyme composed of one OsGGPPS1 subunit and GGPPS recruiting protein (OsGRP). OsGRP is structurally most similar to members of the geranyl diphosphate synthase small subunit type II subfamily. In contrast to members of this subfamily, OsGRP enhances OsGGPPS1 catalytic efficiency and specificity of GGPP production on interaction with OsGGPPS1. Structural biology and protein interaction analyses demonstrate that affinity between OsGRP and OsGGPPS1 is stronger than between two OsGGPPS1 molecules in homodimers. OsGRP determines OsGGPPS1 suborganellar localization and directs it to a large protein complex in thylakoid membranes, consisting of geranylgeranyl reductase (OsGGR), light-harvesting-like protein 3 (OsLIL3), protochlorophyllide oxidoreductase (OsPORB), and chlorophyll synthase (OsCHLG). Taken together, genetic and biochemical analyses suggest OsGRP functions in recruiting OsGGPPS1 from the stroma toward thylakoid membranes, thus providing a mechanism to control GGPP flux toward chlorophyll biosynthesis.
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Caforio A, Driessen AJM. Archaeal phospholipids: Structural properties and biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1325-1339. [PMID: 28007654 DOI: 10.1016/j.bbalip.2016.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023]
Abstract
Phospholipids are major components of the cellular membranes present in all living organisms. They typically form a lipid bilayer that embroiders the cell or cellular organelles, constitute a barrier for ions and small solutes and form a matrix that supports the function of membrane proteins. The chemical composition of the membrane phospholipids present in the two prokaryotic domains Archaea and Bacteria are vastly different. Archaeal lipids are composed of highly-methylated isoprenoid chains that are ether-linked to a glycerol-1-phosphate backbone while bacterial phospholipids consist of straight fatty acids bound by ester bonds to the enantiomeric glycerol-3-phosphate backbone. The chemical structure of the archaeal lipids and their compositional diversity ensures the required stability at extreme environmental conditions as many archaea thrive at such conditions including high or low temperature, high salinity and extreme acidic or alkaline pH values. However, not all archaea are extremophiles, and the presence of ether-linked phospholipids is a phylogenetic marker that distinguishes Archaea from other life forms. During the past decade, our understanding of the biosynthesis of archaeal lipids has progressed resulting in the characterization of the main biosynthetic steps of the pathway including the reconstitution of lipid biosynthesis in vitro. Here we describe the chemical and physical properties of archaeal lipids and membranes derived thereof, summarize the existing knowledge about the enzymology of the archaeal lipid biosynthetic pathway and discuss evolutionary theories associated with the "Lipid Divide" that resulted in the differentiation of bacterial and archaeal organisms. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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15
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AglH, a thermophilic UDP-N-acetylglucosamine-1-phosphate:dolichyl phosphate GlcNAc-1-phosphotransferase initiating protein N-glycosylation pathway in Sulfolobus acidocaldarius, is capable of complementing the eukaryal Alg7. Extremophiles 2016; 21:121-134. [PMID: 27822701 PMCID: PMC5222938 DOI: 10.1007/s00792-016-0890-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/24/2016] [Indexed: 10/31/2022]
Abstract
AglH, a predicted UDP-GlcNAc-1-phosphate:dolichyl phosphate GlcNAc-1-phosphotransferase, is initiating the protein N-glycosylation pathway in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. AglH successfully replaced the endogenous GlcNAc-1-phosphotransferase activity of Alg7 in a conditional lethal Saccharomyces cerevisiae strain, in which the first step of the eukaryal protein N-glycosylation process was repressed. This study is one of the few examples of cross-domain complementation demonstrating a conserved polyprenyl phosphate transferase reaction within the eukaryal and archaeal domain like it was demonstrated for Methanococcus voltae (Shams-Eldin et al. 2008). The topology prediction and the alignment of the AglH membrane protein with GlcNAc-1-phosphotransferases from the three domains of life show significant conservation of amino acids within the different proposed cytoplasmic loops. Alanine mutations of selected conserved amino acids in the putative cytoplasmic loops II (D100), IV (F220) and V (F264) demonstrated the importance of these amino acids for cross-domain AlgH activity in in vitro complementation assays in S. cerevisiae. Furthermore, antibiotic treatment interfering directly with the activity of dolichyl phosphate GlcNAc-1-phosphotransferases confirmed the essentiality of N-glycosylation for cell survival.
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16
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Wang C, Chen Q, Fan D, Li J, Wang G, Zhang P. Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants. MOLECULAR PLANT 2016; 9:195-204. [PMID: 26537048 DOI: 10.1016/j.molp.2015.10.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 05/06/2023]
Abstract
Terpenoids are the largest and most diverse class of plant-specialized metabolites, which function in diverse physiological processes during plant development. In the biosynthesis of plant terpenoids, short-chain prenyltransferases (SC-PTs), together with terpene synthases (TPSs), play critical roles in determining terpenoid diversity. SC-PTs biosynthesize prenyl pyrophosphates with different chain lengths, and these compounds are the direct precursors of terpenoids. Arabidopsis thaliana possesses a subgroup of SC-PTs whose functions are not clearly known. In this study, we focus on 10 geranylgeranyl pyrophosphate synthase-like [GGPPSL] proteins, which are commonly thought to produce GGPP [C20]. We found that a subset of members of the Arabidopsis GGPPSL gene family have undergone neo-functionalization: GGPPSL6, 7, 9, and 10 mainly have geranylfarnesyl pyrophosphate synthase activity (C25; renamed AtGFPPS1, 2, 3, and 4), and GGPPSL8 produces even longer chain prenyl pyrophosphate (≥ C30; renamed polyprenyl pyrophosphate synthase 2, AtPPPS2). By solving the crystal structures of AtGFPPS2, AtPPPS2, and AtGGPPS11, we reveal the product chain-length determination mechanism of SC-PTs and interpret it as a "three floors" model. Using this model, we identified a novel GFPPS clade distributed in Brassicaceae plants and found that the GFPPS gene typically occurs in tandem with a gene encoding a TPS, forming a GFPPS-TPS gene cluster.
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Affiliation(s)
- Chengyuan Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qingwen Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dongjie Fan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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17
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Nagel R, Bernholz C, Vranová E, Košuth J, Bergau N, Ludwig S, Wessjohann L, Gershenzon J, Tissier A, Schmidt A. Arabidopsis thaliana isoprenyl diphosphate synthases produce the C25 intermediate geranylfarnesyl diphosphate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:847-59. [PMID: 26505977 DOI: 10.1111/tpj.13064] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/11/2015] [Accepted: 10/21/2015] [Indexed: 05/22/2023]
Abstract
Isoprenyl diphosphate synthases (IDSs) catalyze some of the most basic steps in terpene biosynthesis by producing the prenyl diphosphate precursors of each of the various terpenoid classes. Most plants investigated have distinct enzymes that produce the short-chain all-trans (E) prenyl diphosphates geranyl diphosphate (GDP, C10 ), farnesyl diphosphate (FDP, C15 ) or geranylgeranyl diphosphate (GGDP, C20 ). In the genome of Arabidopsis thaliana, 15 trans-product-forming IDSs are present. Ten of these have recently been shown to produce GGDP by genetic complementation of a carotenoid pathway engineered into Escherichia coli. When verifying the product pattern of IDSs producing GGDP by a new LC-MS/MS procedure, we found that five of these IDSs produce geranylfarnesyl diphosphate (GFDP, C25 ) instead of GGDP as their major product in enzyme assays performed in vitro. Over-expression of one of the GFDP synthases in A. thaliana confirmed the production of GFDP in vivo. Enzyme assays with A. thaliana protein extracts from roots but not other organs showed formation of GFDP. Furthermore, GFDP itself was detected in root extracts. Subcellular localization studies in leaves indicated that four of the GFDP synthases were targeted to the plastoglobules of the chloroplast and one was targeted to the mitochondria. Sequence comparison and mutational studies showed that the size of the R group of the 5th amino acid residue N-terminal to the first aspartate-rich motif is responsible for C25 versus C20 product formation, with smaller R groups (Ala and Ser) resulting in GGDP (C20 ) as a product and a larger R group (Met) resulting in GFDP (C25 ).
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Affiliation(s)
- Raimund Nagel
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
| | - Carolin Bernholz
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Eva Vranová
- Institute of Biology and Ecology, Pavol Jozef Šafárik University Košice, Mánesova 23, 04154 Košice, Slovakia
| | - Ján Košuth
- Institute of Biology and Ecology, Pavol Jozef Šafárik University Košice, Mánesova 23, 04154 Košice, Slovakia
| | - Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Steve Ludwig
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Ludger Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans Knoell Straße 8, D-07745 Jena, Germany
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18
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Cloning and characterization of farnesyl pyrophosphate synthase from the highly branched isoprenoid producing diatom Rhizosolenia setigera. Sci Rep 2015; 5:10246. [PMID: 25996801 PMCID: PMC4440519 DOI: 10.1038/srep10246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/07/2015] [Indexed: 12/24/2022] Open
Abstract
The diatom Rhizosolenia setigera Brightwell produces highly branched isoprenoid (HBI) hydrocarbons that are ubiquitously present in marine environments. The hydrocarbon composition of R. setigera varies between C25 and C30 HBIs depending on the life cycle stage with regard to auxosporulation. To better understand how these hydrocarbons are biosynthesized, we characterized the farnesyl pyrophosphate (FPP) synthase (FPPS) enzyme of R. setigera. An isolated 1465-bp cDNA clone contained an open reading frame spanning 1299-bp encoding a protein with 432 amino acid residues. Expression of the RsFPPS cDNA coding region in Escherichia coli produced a protein that exhibited FPPS activity in vitro. A reduction in HBI content from diatoms treated with an FPPS inhibitor, risedronate, suggested that RsFPPS supplies precursors for HBI biosynthesis. Product analysis by gas chromatography-mass spectrometry also revealed that RsFPPS produced small amounts of the cis-isomers of geranyl pyrophosphate and FPP, candidate precursors for the cis-isomers of HBIs previously characterized. Furthermore, RsFPPS gene expression at various life stages of R. setigera in relation to auxosporulation were also analyzed. Herein, we present data on the possible role of RsFPPS in HBI biosynthesis, and it is to our knowledge the first instance that an FPPS was cloned and characterized from a diatom.
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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: 263] [Impact Index Per Article: 29.2] [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.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, 409 Latham Hall, 24061, Blacksburg, VA, USA,
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20
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Jain S, Caforio A, Driessen AJM. Biosynthesis of archaeal membrane ether lipids. Front Microbiol 2014; 5:641. [PMID: 25505460 PMCID: PMC4244643 DOI: 10.3389/fmicb.2014.00641] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 01/05/2023] Open
Abstract
A vital function of the cell membrane in all living organism is to maintain the membrane permeability barrier and fluidity. The composition of the phospholipid bilayer is distinct in archaea when compared to bacteria and eukarya. In archaea, isoprenoid hydrocarbon side chains are linked via an ether bond to the sn-glycerol-1-phosphate backbone. In bacteria and eukarya on the other hand, fatty acid side chains are linked via an ester bond to the sn-glycerol-3-phosphate backbone. The polar head groups are globally shared in the three domains of life. The unique membrane lipids of archaea have been implicated not only in the survival and adaptation of the organisms to extreme environments but also to form the basis of the membrane composition of the last universal common ancestor (LUCA). In nature, a diverse range of archaeal lipids is found, the most common are the diether (or archaeol) and the tetraether (or caldarchaeol) lipids that form a monolayer. Variations in chain length, cyclization and other modifications lead to diversification of these lipids. The biosynthesis of these lipids is not yet well understood however progress in the last decade has led to a comprehensive understanding of the biosynthesis of archaeol. This review describes the current knowledge of the biosynthetic pathway of archaeal ether lipids; insights on the stability and robustness of archaeal lipid membranes; and evolutionary aspects of the lipid divide and the LUCA. It examines recent advances made in the field of pathway reconstruction in bacteria.
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Affiliation(s)
- Samta Jain
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
| | - Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen Netherlands ; The Zernike Institute for Advanced Materials, University of Groningen, Groningen Netherlands
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21
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Heider SAE, Peters-Wendisch P, Beekwilder J, Wendisch VF. IdsA is the major geranylgeranyl pyrophosphate synthase involved in carotenogenesis in Corynebacterium glutamicum. FEBS J 2014; 281:4906-20. [PMID: 25181035 DOI: 10.1111/febs.13033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/16/2014] [Accepted: 08/29/2014] [Indexed: 11/27/2022]
Abstract
Corynebacterium glutamicum, a yellow-pigmented soil bacterium that synthesizes the rare cyclic C50 carotenoid decaprenoxanthin and its glucosides, has been engineered for the production of various carotenoids. CrtE was assumed to be the major geranylgeranyl pyrophosphate (GGPP) synthase in carotenogenesis; however, deletion of crtE did not abrogate carotenoid synthesis. In silico analysis of the repertoire of prenyltransferases encoded by the C. glutamicum genome revealed two candidate GGPPS genes (idsA and ispB). The absence of pigmentation of an idsA deletion mutant and complementation experiments with a double deletion mutant lacking both idsA and crtE showed that IdsA is the major GGPPS of C. glutamicum and that crtE overexpression compensated for the lack of IdsA, whereas plasmid-borne overexpression of ispB did not. Purified His-tagged CrtE was active as a homodimer, whereas the active form of IdsA was homotetrameric. Both enzymes catalyzed prenyl transfer with isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate, geranyl pyrophosphate and farnesylphosphate (FPP) as substrates. IdsA showed the highest catalytic efficiency with dimethylallyl pyrophosphate and IPP, whereas the catalytic efficiency of CrtE was highest with geranyl pyrophosphate and IPP. Finally, application of prenyltransferase overexpression revealed that combined overexpression of idsA and the IPP isomerase gene idi in the absence of crtE led to the highest decaprenoxanthin titer reported to date.
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Affiliation(s)
- Sabine A E Heider
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Germany
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22
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Jarrell KF, Ding Y, Meyer BH, Albers SV, Kaminski L, Eichler J. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis. Microbiol Mol Biol Rev 2014; 78:304-41. [PMID: 24847024 PMCID: PMC4054257 DOI: 10.1128/mmbr.00052-13] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Yan Ding
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lina Kaminski
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel
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Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A 2013; 110:E1196-202. [PMID: 23493556 DOI: 10.1073/pnas.1300632110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value ≤ 1e(-70)) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.
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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]
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25
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Phylogenomic investigation of phospholipid synthesis in archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:630910. [PMID: 23304072 PMCID: PMC3533463 DOI: 10.1155/2012/630910] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/03/2012] [Indexed: 12/22/2022]
Abstract
Archaea have idiosyncratic cell membranes usually based on phospholipids containing glycerol-1-phosphate linked by ether bonds to isoprenoid lateral chains. Since these phospholipids strongly differ from those of bacteria and eukaryotes, the origin of the archaeal membranes (and by extension, of all cellular membranes) was enigmatic and called for accurate evolutionary studies. In this paper we review some recent phylogenomic studies that have revealed a modified mevalonate pathway for the synthesis of isoprenoid precursors in archaea and suggested that this domain uses an atypical pathway of synthesis of fatty acids devoid of any acyl carrier protein, which is essential for this activity in bacteria and eukaryotes. In addition, we show new or updated phylogenetic analyses of enzymes likely responsible for the isoprenoid chain synthesis from their precursors and the phospholipid synthesis from glycerol phosphate, isoprenoids, and polar head groups. These results support that most of these enzymes can be traced back to the last archaeal common ancestor and, in many cases, even to the last common ancestor of all living organisms.
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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.
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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
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27
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Characterization of the AggR regulon in enteroaggregative Escherichia coli. Infect Immun 2012; 81:122-32. [PMID: 23090962 DOI: 10.1128/iai.00676-12] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AggR is a transcriptional regulator of enteroaggregative Escherichia coli (EAEC) and has been proposed as the defining factor for typical EAEC strains. Expression of multiple putative virulence factors, including the aggregative adherence fimbriae (AAF), dispersin, the dispersin translocator Aat, and the Aai type VI secretion system, have been found to be regulated by AggR. Here, we confirm the existence of at least 44 AggR-regulated genes using DNA microarray and real-time quantitative reverse transcription-PCR (qRT-PCR); these genes include chromosomal and plasmid-borne loci and 19 previously unsuspected genes. Two previously uncharacterized virulence plasmid-encoded open reading frames (ORFs) (designated ORF3 and ORF4) exhibit significant identity with isoprenoid biosynthesis genes of Bacteria and Archaea. The predicted ORF4 product is closely related to isopentenyl isomerase (IDI) enzymes, whereas the predicted product of the adjacent ORF3 exhibits an aspartate-rich region that is common among trans-isoprenyl phosphate synthases. We show that mutations in these ORFs confer changes in bacterial surface properties. AggR coordinately controls expression of a large number of EAEC genes.
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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.
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Affiliation(s)
- Zhu-Hong Li
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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29
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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]
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30
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Structure and Mutation Analysis of Archaeal Geranylgeranyl Reductase. J Mol Biol 2011; 409:543-57. [DOI: 10.1016/j.jmb.2011.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/26/2011] [Accepted: 04/01/2011] [Indexed: 11/19/2022]
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31
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Tholl D, Lee S. Terpene Specialized Metabolism in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2011; 9:e0143. [PMID: 22303268 PMCID: PMC3268506 DOI: 10.1199/tab.0143] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C(5)-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C(20)-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C(10)-, C(15)-, and C(20)-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Sungbeom Lee
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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32
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Hsieh FL, Chang TH, Ko TP, Wang AHJ. Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase. PLANT PHYSIOLOGY 2011; 155:1079-90. [PMID: 21220764 PMCID: PMC3046570 DOI: 10.1104/pp.110.168799] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/06/2011] [Indexed: 05/19/2023]
Abstract
Prenyltransferases (PTSs) are involved in the biosynthesis of terpenes with diverse functions. Here, a novel PTS from Arabidopsis (Arabidopsis thaliana) is identified as a trans-type polyprenyl pyrophosphate synthase (AtPPPS), which forms a trans-double bond during each homoallylic substrate condensation, rather than a homomeric C10-geranyl pyrophosphate synthase as originally proposed. Biochemical and genetic complementation analyses indicate that AtPPPS synthesizes C25 to C45 medium/long-chain products. Its close relationship to other long-chain PTSs is also uncovered by phylogenetic analysis. A mutant of contiguous surface polar residues was produced by replacing four charged surface amino acids with alanines to facilitate the crystallization of the enzyme. The crystal structures of AtPPPS determined here in apo and ligand-bound forms further reveal an active-site cavity sufficient to accommodate the medium/long-chain products. The two monomers in each dimer adopt different conformations at the entrance of the active site depending on the binding of substrates. Taken together, these results suggest that AtPPPS is endowed with a unique functionality among the known PTSs.
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33
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Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K. Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. J Biol Chem 2010; 286:3729-40. [PMID: 21068379 DOI: 10.1074/jbc.m110.147991] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 (Ml-HexPPs) is a heterooligomeric type trans-prenyltransferase catalyzing consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates (C(5)) on a farnesyl diphosphate (FPP; C(15)) to form an (all-E) hexaprenyl diphosphate (HexPP; C(30)). Ml-HexPPs is known to function as a heterodimer of two different subunits, small and large subunits called HexA and HexB, respectively. Compared with homooligomeric trans-prenyltransferases, the molecular mechanism of heterooligomeric trans-prenyltransferases is not yet clearly understood, particularly with respect to the role of the small subunits lacking the catalytic motifs conserved in most known trans-prenyltransferases. We have determined the crystal structure of Ml-HexPPs both in the substrate-free form and in complex with 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate ammonium salt (3-DesMe-FPP), an analog of FPP. The structure of HexB is composed of mostly antiparallel α-helices joined by connecting loops. Two aspartate-rich motifs (designated the first and second aspartate-rich motifs) and the other characteristic motifs in HexB are located around the diphosphate part of 3-DesMe-FPP. Despite the very low amino acid sequence identity and the distinct polypeptide chain lengths between HexA and HexB, the structure of HexA is quite similar to that of HexB. The aliphatic tail of 3-DesMe-FPP is accommodated in a large hydrophobic cleft starting from HexB and penetrating to the inside of HexA. These structural features suggest that HexB catalyzes the condensation reactions and that HexA is directly involved in the product chain length control in cooperation with HexB.
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Affiliation(s)
- Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8502, Japan
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Matsumi R, Atomi H, Driessen AJM, van der Oost J. Isoprenoid biosynthesis in Archaea--biochemical and evolutionary implications. Res Microbiol 2010; 162:39-52. [PMID: 21034816 DOI: 10.1016/j.resmic.2010.10.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Isoprenoids are indispensable for all types of cellular life in the Archaea, Bacteria, and Eucarya. These membrane-associated molecules are involved in a wide variety of vital biological functions, ranging from compartmentalization and stability, to protection and energy-transduction. In Archaea, isoprenoid compounds constitute the hydrophobic moiety of the typical ether-linked membrane lipids. With respect to stereochemistry and composition, these archaeal lipids are very different from the ester-linked, fatty acid-based phospholipids in bacterial and eukaryotic membranes. This review provides an update on isoprenoid biosynthesis pathways, with a focus on the archaeal enzymes. The black-and-white distribution of fundamentally distinct membrane lipids in Archaea on the one hand, and Bacteria and Eucarya on the other, has previously been used as a basis for hypothetical evolutionary scenarios, a selection of which will be discussed here.
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Affiliation(s)
- Rie Matsumi
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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Hsieh FL, Chang TH, Ko TP, Wang AHJ. Enhanced specificity of mint geranyl pyrophosphate synthase by modifying the R-loop interactions. J Mol Biol 2010; 404:859-73. [PMID: 20965200 DOI: 10.1016/j.jmb.2010.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/07/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
Abstract
Isoprenoids, most of them synthesized by prenyltransferases (PTSs), are a class of important biologically active compounds with diverse functions. The mint geranyl pyrophosphate synthase (GPPS) is a heterotetramer composed of two LSU·SSU (large/small subunit) dimers. In addition to C(10)-GPP, the enzyme also produces geranylgeranyl pyrophosphate (C(20)-GGPP) in vitro, probably because of the conserved active-site structures between the LSU of mint GPPS and the homodimeric GGPP synthase from mustard. By contrast, the SSU lacks the conserved aspartate-rich motifs for catalysis. A major active-site cavity loop in the LSU and other trans-type PTSs is replaced by the regulatory R-loop in the SSU. Only C(10)-GPP, but not C(20)-GGPP, was produced when intersubunit interactions of the R-loop were disrupted by either deletion or multiple point mutations. The structure of the deletion mutant, determined in two different crystal forms, shows an intact (LSU·SSU)(2) heterotetramer, as previously observed in the wild-type enzyme. The active-site of LSU remains largely unaltered, except being slightly more open to the bulk solvent. The R-loop of SSU acts by regulating the product release from LSU, just as does its equivalent loop in a homodimeric PTS, which prevents the early reaction intermediates from escaping the active site of the other subunit. In this way, the product-retaining function of R-loop provides a more stringent control for chain-length determination, complementary to the well-established molecular ruler mechanism. We conclude that the R-loop may be used not only to conserve the GPPS activity but also to produce portions of C(20)-GGPP in mint.
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Affiliation(s)
- Fu-Lien Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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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]
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37
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Chang TH, Hsieh FL, Ko TP, Teng KH, Liang PH, Wang AHJ. Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation. THE PLANT CELL 2010; 22:454-67. [PMID: 20139160 PMCID: PMC2845413 DOI: 10.1105/tpc.109.071738] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Terpenes (isoprenoids), derived from isoprenyl pyrophosphates, are versatile natural compounds that act as metabolism mediators, plant volatiles, and ecological communicators. Divergent evolution of homomeric prenyltransferases (PTSs) has allowed PTSs to optimize their active-site pockets to achieve catalytic fidelity and diversity. Little is known about heteromeric PTSs, particularly the mechanisms regulating formation of specific products. Here, we report the crystal structure of the (LSU . SSU)(2)-type (LSU/SSU = large/small subunit) heterotetrameric geranyl pyrophosphate synthase (GPPS) from mint (Mentha piperita). The LSU and SSU of mint GPPS are responsible for catalysis and regulation, respectively, and this SSU lacks the essential catalytic amino acid residues found in LSU and other PTSs. Whereas no activity was detected for individually expressed LSU or SSU, the intact (LSU . SSU)(2) tetramer produced not only C(10)-GPP at the beginning of the reaction but also C(20)-GGPP (geranylgeranyl pyrophosphate) at longer reaction times. The activity for synthesizing C(10)-GPP and C(20)-GGPP, but not C(15)-farnesyl pyrophosphate, reflects a conserved active-site structure of the LSU and the closely related mustard (Sinapis alba) homodimeric GGPPS. Furthermore, using a genetic complementation system, we showed that no C(20)-GGPP is produced by the mint GPPS in vivo. Presumably through protein-protein interactions, the SSU remodels the active-site cavity of LSU for synthesizing C(10)-GPP, the precursor of volatile C(10)-monoterpenes.
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Affiliation(s)
- Tao-Hsin Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
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Schmidt A, Wächtler B, Temp U, Krekling T, Séguin A, Gershenzon J. A bifunctional geranyl and geranylgeranyl diphosphate synthase is involved in terpene oleoresin formation in Picea abies. PLANT PHYSIOLOGY 2010; 152:639-55. [PMID: 19939949 PMCID: PMC2815902 DOI: 10.1104/pp.109.144691] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 11/19/2009] [Indexed: 05/19/2023]
Abstract
The conifer Picea abies (Norway spruce) defends itself against herbivores and pathogens with a terpenoid-based oleoresin composed chiefly of monoterpenes (C(10)) and diterpenes (C(20)). An important group of enzymes in oleoresin biosynthesis are the short-chain isoprenyl diphosphate synthases that produce geranyl diphosphate (C(10)), farnesyl diphosphate (C(15)), and geranylgeranyl diphosphate (C(20)) as precursors of different terpenoid classes. We isolated a gene from P. abies via a homology-based polymerase chain reaction approach that encodes a short-chain isoprenyl diphosphate synthase making an unusual mixture of two products, geranyl diphosphate (C(10)) and geranylgeranyl diphosphate (C(20)). This bifunctionality was confirmed by expression in both prokaryotic (Escherichia coli) and eukaryotic (P. abies embryogenic tissue) hosts. Thus, this isoprenyl diphosphate synthase, designated PaIDS1, could contribute to the biosynthesis of both major terpene types in P. abies oleoresin. In saplings, PaIDS1 transcript was restricted to wood and bark, and transcript level increased dramatically after methyl jasmonate treatment, which induces the formation of new (traumatic) resin ducts. Polyclonal antibodies localized the PaIDS1 protein to the epithelial cells surrounding the traumatic resin ducts. PaIDS1 has a close phylogenetic relationship to single-product conifer geranyl diphosphate and geranylgeranyl diphosphate synthases. Its catalytic properties and reaction mechanism resemble those of conifer geranylgeranyl diphosphate synthases, except that significant quantities of the intermediate geranyl diphosphate are released. Using site-directed mutagenesis and chimeras of PaIDS1 with single-product geranyl diphosphate and geranylgeranyl diphosphate synthases, specific amino acid residues were identified that alter the relative composition of geranyl to geranylgeranyl diphosphate.
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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.
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Affiliation(s)
- Wolfgang Brandt
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Halle (Saale), Germany.
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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.
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Affiliation(s)
- A Huma Taban
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada 89557-0014, USA
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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]
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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]
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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.
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Affiliation(s)
- Motoyoshi Noike
- Department of Biochemistry and Engineering, Graduate School of Engineering, Tohoku University, Miyagi, Japan
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Koga Y, Morii H. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev 2007; 71:97-120. [PMID: 17347520 PMCID: PMC1847378 DOI: 10.1128/mmbr.00033-06] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This review deals with the in vitro biosynthesis of the characteristics of polar lipids in archaea along with preceding in vivo studies. Isoprenoid chains are synthesized through the classical mevalonate pathway, as in eucarya, with minor modifications in some archaeal species. Most enzymes involved in the pathway have been identified enzymatically and/or genomically. Three of the relevant enzymes are found in enzyme families different from the known enzymes. The order of reactions in the phospholipid synthesis pathway (glycerophosphate backbone formation, linking of glycerophosphate with two radyl chains, activation by CDP, and attachment of common polar head groups) is analogous to that of bacteria. sn-Glycerol-1-phosphate dehydrogenase is responsible for the formation of the sn-glycerol-1-phosphate backbone of phospholipids in all archaea. After the formation of two ether bonds, CDP-archaeol acts as a common precursor of various archaeal phospholipid syntheses. Various phospholipid-synthesizing enzymes from archaea and bacteria belong to the same large CDP-alcohol phosphatidyltransferase family. In short, the first halves of the phospholipid synthesis pathways play a role in synthesis of the characteristic structures of archaeal and bacterial phospholipids, respectively. In the second halves of the pathways, the polar head group-attaching reactions and enzymes are homologous in both domains. These are regarded as revealing the hybrid nature of phospholipid biosynthesis. Precells proposed by Wächtershäuser are differentiated into archaea and bacteria by spontaneous segregation of enantiomeric phospholipid membranes (with sn-glycerol-1-phosphate and sn-glycerol-3-phosphate backbones) and the fusion and fission of precells. Considering the nature of the phospholipid synthesis pathways, we here propose that common phospholipid polar head groups were present in precells before the differentiation into archaea and bacteria.
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Affiliation(s)
- Yosuke Koga
- Department of Chemistry, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan.
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Poznański J, Szkopinska A. Precise bacterial polyprenol length control fails inSaccharomyces cerevisiae. Biopolymers 2007; 86:155-64. [PMID: 17345630 DOI: 10.1002/bip.20715] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A comparison of amino acid sequences of yeast Rer2p and Srt1p Z-prenyltransferases shows that the spatial organization of their substrate tunnels agrees with that determined by X-ray for the E. coli undecaprenyl diphosphate synthase (UPPs). The observed trend in the maxima of product length distribution shifted from C(55) in UPPs to C(80) in Rer2p and to C(110) in Srt1p. This suggests a significant increase in the size of the enzyme hydrophobic tunnel from approximately 1000 A(3) of E. coli UPPs to approximately 1300 A(3) required to accommodate C(80) in Rer2p and to 1700 A(3) for C(110) in Srt1p. Moreover, Srt1p products reaching C(290) indicate the failure of a strict bacterial-like chain length control. On the basis of E. coli UPPs crystallographic structure the yeast Rer2p model was constructed. In the model three amino acid residues inserted into the sequence corresponding to the "floor" region of the tunnel extends the bottom loop what results in the required increase of the tunnel volume. Moreover, thermal fluctuations of this loop occasionally create a hole in the tunnel floor, making escape of polyprenol omega end out of the tunnel possible what switches off the control mechanism of product length thereby allowing a practically unlimited elongation process leading to an exponential distribution of longer chain polyprenols.
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Affiliation(s)
- Jarosław Poznański
- Institute of Biochemistry and Biophysics PAS, ul. Pawinskiego 5a, 02-106 Warszawa, Poland
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Cusson M, Béliveau C, Sen SE, Vandermoten S, Rutledge RG, Stewart D, Francis F, Haubruge E, Rehse P, Huggins DJ, Dowling APG, Grant GH. Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: Implications for the biosynthesis of ethyl-substituted juvenile hormones. Proteins 2006; 65:742-58. [PMID: 16972283 DOI: 10.1002/prot.21057] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The sesquiterpenoid juvenile hormone (JH) regulates insect development and reproduction. Most insects produce only one chemical form of JH, but the Lepidoptera produce four derivatives featuring ethyl branches. The biogenesis of these JHs requires the synthesis of ethyl-substituted farnesyl diphosphate (FPP) by FPP synthase (FPPS). To determine if there exist more than one lepidopteran FPPS, and whether one FPPS homolog is better adapted for binding the bulkier ethyl-branched substrates/products, we cloned three lepidopteran FPPS cDNAs, two from Choristoneura fumiferana and one from Pseudaletia unipuncta. Amino acid sequence comparisons among these and other eukaryotic FPPSs led to the recognition of two lepidopteran FPPS types. Type-I FPPSs display unique active site substitutions, including several in and near the first aspartate-rich motif, whereas type-II proteins have a more "conventional" catalytic cavity. In a yeast assay, a Drosophila FPPS clone provided full complementation of an FPPS mutation, but lepidopteran FPPS clones of either type yielded only partial complementation, suggesting unusual catalytic features and/or requirements of these enzymes. Although a structural analysis of lepidopteran FPPS active sites suggested that type-I enzymes are better suited than type-II for generating ethyl-substituted products, a quantitative real-time PCR assessment of their relative abundance in insect tissues indicated that type-I expression is ubiquitous whereas that of type-II is essentially confined to the JH-producing glands, where its transcripts are approximately 20 times more abundant than those of type-I. These results suggest that type-II FPPS plays a leading role in lepidopteran JH biosynthesis in spite of its apparently more conventional catalytic cavity.
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Affiliation(s)
- Michel Cusson
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec City, Québec G1V 4C7, Canada.
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Sun J, Aoki K, Wang W, Guo A, Misumi J. Sodium nitrite-induced cytotoxicity in cultured human gastric epithelial cells. Toxicol In Vitro 2006; 20:1133-8. [PMID: 16581224 DOI: 10.1016/j.tiv.2006.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 01/07/2006] [Accepted: 02/20/2006] [Indexed: 11/25/2022]
Abstract
To investigate the effect of sodium nitrite on the viability of the human gastric adenocarcinoma epithelial cell line, AGS, cultured AGS cells were exposed to various concentrations of sodium nitrite for 24, 48 or 72 h. The cytotoxic response was assessed using a cell proliferation assay, and the extent of the response was evaluated on the basis of intracellular and extracellular levels of interleukin 1 beta (IL-1 beta), interleukin 6 (IL-6), interleukin 8 (IL-8) and tumor necrosis factor (TNF-alpha). Both mRNA and protein levels were measured for each cytokine. Sodium nitrite had a significant effect on AGS cell proliferation after a 72-h exposure. At low sodium nitrite concentrations (up to 6.25 mM), cell proliferation increased in a dose-dependent manner; however, exposure to higher concentrations resulted in a dose-dependent decrease in cell proliferation. Sodium nitrite at a low concentration (6.25 mM) increased IL-8 release, whereas IL-1 beta, IL-6, and TNF-alpha release increased only after exposure to high sodium nitrite concentration (25 mM). Our data demonstrate that sodium nitrite can induce the release of these inflammatory cytokines and that high concentrations of sodium nitrite decrease AGS cell proliferation.
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Affiliation(s)
- Juan Sun
- School of Public Health and Family Medicine, Capital University of Medical Sciences, Beijing, China.
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Sun HY, Ko TP, Kuo CJ, Guo RT, Chou CC, Liang PH, Wang AHJ. Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures. J Bacteriol 2005; 187:8137-48. [PMID: 16291686 PMCID: PMC1291270 DOI: 10.1128/jb.187.23.8137-8148.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hexaprenyl pyrophosphate synthase (HexPPs) from Sulfolobus solfataricus catalyzes the synthesis of trans-C(30)-hexaprenyl pyrophosphate (HexPP) by reacting two isopentenyl pyrophosphate molecules with one geranylgeranyl pyrophosphate. The crystal structure of the homodimeric C(30)-HexPPs resembles those of other trans-prenyltransferases, including farnesyl pyrophosphate synthase (FPPs) and octaprenyl pyrophosphate synthase (OPPs). In both subunits, 10 core helices are arranged about a central active site cavity. Leu164 in the middle of the cavity controls the product chain length. Two protein conformers are observed in the S. solfataricus HexPPs structure, and the major difference between them occurs in the flexible region of residues 84 to 100. Several helices (alphaI, alphaJ, alphaK, and part of alphaH) and the associated loops have high-temperature factors in one monomer, which may be related to the domain motion that controls the entrance to the active site. Different side chain conformations of Trp136 in two HexPPs subunits result in weaker hydrophobic interactions at the dimer interface, in contrast to the symmetric pi-pi stacking interactions of aromatic side chains found in FPPs and OPPs. Finally, the three-conformer switched model may explain the catalytic process for HexPPs.
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Affiliation(s)
- Han-Yu Sun
- Institute of Biochemical Sciences, National Taiwan University, Taipei
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Fukusaki EI, Nishikawa T, Kato K, Shinmyo A, Hemmi H, Nishino T, Kobayashi A. Introduction of the archaebacterial geranylgeranyl pyrophosphate synthase gene into Chlamydomonas reinhardtii chloroplast. J Biosci Bioeng 2005; 95:283-7. [PMID: 16233406 DOI: 10.1016/s1389-1723(03)80030-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 11/15/2002] [Indexed: 11/23/2022]
Abstract
Geranylgeranyl pyrophosphate (GGPP) synthase gene (gds) derived from a thermophilic Archae Sulfolobus acidocaldarius, was introduced into a unicellular green alga Chlamydomonas reinhardtii chloroplast. Heat treatment abolished the prenyltransferase activity of the wild strain, but the activity of the transforment remained. The transformant accumulated gds gene mRNA and translation product.
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Affiliation(s)
- Ei-Ichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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Abstract
Isoprenoids represent the oldest class of known low molecular-mass natural products synthesized by plants. Their biogenesis in plastids, mitochondria and the endoplasmic reticulum-cytosol proceed invariably from the C5 building blocks, isopentenyl diphosphate and/or dimethylallyl diphosphate according to complex and reiterated mechanisms. Compounds derived from the pathway exhibit a diverse spectrum of biological functions. This review centers on advances obtained in the field based on combined use of biochemical, molecular biology and genetic approaches. The function and evolutionary implications of this metabolism are discussed in relation with seminal informations gathered from distantly but related organisms.
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Affiliation(s)
- Florence Bouvier
- Institut de Biologie Moléculaire des Plantes du CNRS (UPR2357) et Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
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