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Germann AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P, Axmann IM. A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2023; 14:1024981. [PMID: 37324717 PMCID: PMC10266222 DOI: 10.3389/fpls.2023.1024981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacteria are a promising platform for the production of the triterpene squalene (C30), a precursor for all plant and animal sterols, and a highly attractive intermediate towards triterpenoids, a large group of secondary plant metabolites. Synechocystis sp. PCC 6803 natively produces squalene from CO2 through the MEP pathway. Based on the predictions of a constraint-based metabolic model, we took a systematic overexpression approach to quantify native Synechocystis gene's impact on squalene production in a squalene-hopene cyclase gene knock-out strain (Δshc). Our in silico analysis revealed an increased flux through the Calvin-Benson-Bassham cycle in the Δshc mutant compared to the wildtype, including the pentose phosphate pathway, as well as lower glycolysis, while the tricarboxylic acid cycle predicted to be downregulated. Further, all enzymes of the MEP pathway and terpenoid synthesis, as well as enzymes from the central carbon metabolism, Gap2, Tpi and PyrK, were predicted to positively contribute to squalene production upon their overexpression. Each identified target gene was integrated into the genome of Synechocystis Δshc under the control of the rhamnose-inducible promoter Prha. Squalene production was increased in an inducer concentration dependent manner through the overexpression of most predicted genes, which are genes of the MEP pathway, ispH, ispE, and idi, leading to the greatest improvements. Moreover, we were able to overexpress the native squalene synthase gene (sqs) in Synechocystis Δshc, which reached the highest production titer of 13.72 mg l-1 reported for squalene in Synechocystis sp. PCC 6803 so far, thereby providing a promising and sustainable platform for triterpene production.
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Affiliation(s)
- Anna T. Germann
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Nakielski
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maximilian Dietsch
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tim Petzel
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Moser
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Sebastian Triesch
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Philipp Westhoff
- Plant Metabolism and Metabolomics Laboratory, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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2
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Liu C, Zhao Z, Xu Q, Zhang H, Liu X, Yin C, Yan H, Liu Y. Comparative Genomic Analysis of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05 for Producing Macular Pigment. Microorganisms 2023; 11:microorganisms11020266. [PMID: 36838230 PMCID: PMC9967899 DOI: 10.3390/microorganisms11020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Sphingomonas morindae sp. NBD5, which we previously identified and tested, is a new bacterial strain for producing lutein. Here, based on the next-generation sequencing technology, we analyzed high throughput genomic sequences and compared related functional genes of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05. The genome of Sphingomonas morindae sp. NBD5 has two sets of chromosomes, which is 4,239,716 bp and harbors 3882 protein coding genes. There are 59 protein-coding genes related to the macular pigment (MP) biosynthesis, of which four genes (ackA, pgm, gpmI and pckA) are unique. These genes, pckG, porB, meh, and fldA, are unique in Sphingopyxis sp. USTB-05. The analysis of Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05 genomes gives an insight into the new pathway for MP production. These genes for the transformation of glucose to MP were also found in Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05. This study expands the understanding of the pathway for complete biosynthesis of MP by Sphingomonas morindae sp. NBD5 and Sphingopyxis sp. USTB-05.
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Affiliation(s)
| | | | | | | | | | | | - Hai Yan
- Correspondence: (H.Y.); (Y.L.)
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3
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D'Angelo F, Fernández-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Büke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, Bokinsky G. Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 2022; 11:70936. [PMID: 35244541 PMCID: PMC8896826 DOI: 10.7554/elife.70936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways.
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Affiliation(s)
- Francesca D'Angelo
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Elena Fernández-Fueyo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Pierre Simon Garcia
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Helena Shomar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Martin Pelosse
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Rita Rebelo Manuel
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Ferhat Büke
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Siyi Liu
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | - Niels van den Broek
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Nicolas Duraffourg
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Emmanuelle Bouveret
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Béatrice Py
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | | | - Frédéric Barras
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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4
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Henkel S, Frohnecke N, Maus D, McConville MJ, Laue M, Blume M, Seeber F. Toxoplasma gondii apicoplast-resident ferredoxin is an essential electron transfer protein for the MEP isoprenoid-biosynthetic pathway. J Biol Chem 2021; 298:101468. [PMID: 34896149 PMCID: PMC8717598 DOI: 10.1016/j.jbc.2021.101468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/30/2022] Open
Abstract
Apicomplexan parasites, such as Toxoplasma gondii, are unusual in that each cell contains a single apicoplast, a plastid-like organelle that compartmentalizes enzymes involved in the essential 2C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis. The last two enzymatic steps in this organellar pathway require electrons from a redox carrier. However, the small iron-sulfur cluster-containing protein ferredoxin, a likely candidate for this function, has not been investigated in this context. We show here that inducible knockdown of T. gondii ferredoxin results in progressive inhibition of growth and eventual parasite death. Surprisingly, this phenotype is not accompanied by ultrastructural changes in the apicoplast or overall cell morphology. The knockdown of ferredoxin was instead associated with a dramatic decrease in cellular levels of the last two metabolites in isoprenoid biosynthesis, 1-hydroxy-2-methyl-2-(E)- butenyl-4-pyrophosphate, and isomeric dimethylallyl pyrophosphate/isopentenyl pyrophosphate. Ferredoxin depletion was also observed to impair gliding motility, consistent with isoprenoid metabolites being important for dolichol biosynthesis, protein prenylation, and modification of other proteins involved in motility. Significantly, pharmacological inhibition of isoprenoid synthesis of the host cell exacerbated the impact of ferredoxin depletion on parasite replication, suggesting that the slow onset of parasite death after ferredoxin depletion is because of isoprenoid scavenging from the host cell and leading to partial compensation of the depleted parasite metabolites upon ferredoxin knockdown. Overall, these findings show that ferredoxin has an essential physiological function as an electron donor for the 2C-methyl-D-erythritol 4-phosphate pathway and is a potential drug target for apicomplexan parasites.
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Affiliation(s)
- Stephanie Henkel
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany
| | - Nora Frohnecke
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany
| | - Deborah Maus
- Metabolism of Microbial Pathogens (NG2), Robert Koch Institute, Berlin, Germany
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Robert Koch Institute, Berlin, Germany
| | - Martin Blume
- Metabolism of Microbial Pathogens (NG2), Robert Koch Institute, Berlin, Germany; Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Melbourne, Australia
| | - Frank Seeber
- Mycotic and Parasitic Agents and Mycobacteria (FG16), Robert Koch Institute, Berlin, Germany.
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5
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Nguyen AD, Kim D, Lee EY. Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound. Metab Eng 2020; 61:69-78. [PMID: 32387228 DOI: 10.1016/j.ymben.2020.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/21/2020] [Accepted: 04/25/2020] [Indexed: 11/22/2022]
Abstract
Isoprenoids are an abundant and diverse class of natural products with various applications in the pharmaceutical, cosmetics and biofuel industries. A methanotroph-based biorefinery is an attractive scenario for the production of a variety of value-added compounds from methane, because methane is a promising alternative feedstock for industrial biomanufacturing. In this study, we metabolically engineered Methylotuvimicrobium alcaliphilum 20Z for de novo synthesis of a sesquiterpenoid from methane, using α-humulene as a model compound, via optimization of the native methylerythritol phosphate (MEP) pathway. Expression of codon-optimized α-humulene synthase from Zingiber zerumbet in M. alcaliphilum 20Z resulted in an initial yield of 0.04 mg/g dry cell weight. Overexpressing key enzymes (IspA, IspG, and Dxs) for debottlenecking of the MEP pathway increased α-humulene production 5.2-fold compared with the initial strain. Subsequently, redirecting the carbon flux through the Embden-Meyerhof-Parnas pathway resulted in an additional 3-fold increase in α-humulene production. Additionally, a genome-scale model using flux scanning based on enforced objective flux method was used to identify potential overexpression targets to increase flux towards isoprenoid production. Several target reactions from cofactor synthesis pathways were probed and evaluated for their effects on α-humulene synthesis, resulting in α-humulene yield up to 0.75 mg/g DCW with 18.8-fold enhancement from initial yield. This study first demonstrates production of a sesquiterpenoid from methane using methanotrophs as the biocatalyst and proposes potential strategies to enhance production of sesquiterpenoid and related isoprenoid products in engineered methanotrophic bacteria.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea.
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6
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Sudatti DB, Duarte HM, Soares AR, Salgado LT, Pereira RC. New Ecological Role of Seaweed Secondary Metabolites as Autotoxic and Allelopathic. FRONTIERS IN PLANT SCIENCE 2020; 11:347. [PMID: 32523586 PMCID: PMC7261924 DOI: 10.3389/fpls.2020.00347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Allelopathy and autotoxicity are well-known biological processes in angiosperms but are very little explored or even unknown in seaweeds. In this study, extract and major pure compounds from two distinct populations of the red seaweed Laurencia dendroidea were investigated to evaluate the effect of autotoxicity through auto- and crossed experiments under laboratory conditions, using chlorophyll fluorescence imaging to measure inhibition of photosynthesis (ΦPSII) as a variable response. Individuals of L. dendroidea from Azeda beach were inhibited by their own extract (IC50 = 219 μg/ml) and the major compound elatol (IC50 = 87 μg/ml); both chemicals also inhibited this seaweed species from Forno beach (IC50 = 194 μg/ml for the extract and IC50 = 277 μg/ml for elatol). By contrast, the extract of L. dendroidea from Forno and its major compound obtusol showed no inhibitory effect in individuals of both populations; but obtusol was insoluble to be tested at higher concentrations, which could be active as observed for elatol. The Azeda population displayed higher susceptibility to the Azeda extract and to elatol, manifested on the first day, unlike Forno individuals, in which the effect was only detected on the second day; and inhibition of ΦPSII was more pronounced at apical than basal portions of the thalli of L. dendroidea. This first finding of seaweed autotoxicity and allelopathic effects revealed the potential of the chemistry of secondary metabolites for intra- and inter-populational interactions, and for structuring seaweed populations.
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Affiliation(s)
- Daniela Bueno Sudatti
- Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Brazil
| | - Heitor Monteiro Duarte
- Grupo de Produtos Naturais de Organismos Aquáticos (GPNOA), Núcleo de Estudos em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | - Angélica Ribeiro Soares
- Grupo de Produtos Naturais de Organismos Aquáticos (GPNOA), Núcleo de Estudos em Ecologia e Desenvolvimento Sócio-ambiental de Macaé, Universidade Federal do Rio de Janeiro, Macaé, Brazil
| | | | - Renato Crespo Pereira
- Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Brazil
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Campbell IJ, Olmos JL, Xu W, Kahanda D, Atkinson JT, Sparks ON, Miller MD, Phillips GN, Bennett GN, Silberg JJ. Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases. J Biol Chem 2020; 295:10610-10623. [PMID: 32434930 DOI: 10.1074/jbc.ra120.013501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/15/2020] [Indexed: 01/13/2023] Open
Abstract
Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (-336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.
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Affiliation(s)
- Ian J Campbell
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Jose Luis Olmos
- Biochemistry and Cell Biology Graduate Program, Rice University, Houston, Texas, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Weijun Xu
- Department of Biosciences, Rice University, Houston, Texas, USA
| | | | | | | | | | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - George N Bennett
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA .,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA.,Department of Bioengineering, Rice University, Houston, Texas, USA
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8
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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9
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Pala ZR, Saxena V, Saggu GS, Mani SK, Pareek RP, Kochar SK, Kochar DK, Garg S. Functional analysis of iron-sulfur cluster biogenesis (SUF pathway) from Plasmodium vivax clinical isolates. Exp Parasitol 2019; 198:53-62. [PMID: 30721667 DOI: 10.1016/j.exppara.2019.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/29/2018] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
Abstract
Iron-sulfur (Fe-S) clusters are critical metallo-cofactors required for cell function. Assembly of these cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. In Plasmodium, two pathways for these Fe-S cluster biogenesis have been reported; ISC pathway in the mitochondria and SUF pathway functional in the apicoplast. Amongst these, SUF pathway is reported essential for the apicoplast maintenance and parasite survival. Many of its components have been studied from P. falciparum and P. berghei in recent years, still few queries remain to be addressed; one of them being the assembly and transfer of Fe-S clusters. In this study, using P. vivax clinical isolates, we have shown the in vitro interaction of SUF pathway proteins SufS and SufE responsible for sulfur mobilization in the apicoplast. The sulfur mobilized by the SufSE complex assembles on the scaffold protein PvSufA along with iron provided by the external source. Here, we demonstrate in vitro transfer of these labile Fe-S clusters from the scaffold protein on to an apo-protein, PvIspG (a protein involved in penultimate step of Isoprenoids biosynthesis pathway) in order to provide an insight into the interaction of different components for the biosynthesis and transfer of Fe-S clusters. Our analysis indicate that inspite of the presence of variations in pathway proteins, the overall pathway remains well conserved in the clinical isolates when compared to that reported in lab strains.
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Affiliation(s)
- Zarna Rajeshkumar Pala
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
| | - Gagandeep Singh Saggu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Satish Kailasam Mani
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Rajendra Prasad Pareek
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Sanjay Kumar Kochar
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Dhanpat Kumar Kochar
- Department of Medicine, Rajasthan University of Health Sciences, Jaipur, Rajasthan, India
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
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10
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Uchida H, Mizohata E, Okada S. Docking analysis of models for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase and a ferredoxin from Botryococcus braunii, race B. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:297-301. [PMID: 31819737 PMCID: PMC6879371 DOI: 10.5511/plantbiotechnology.18.0601a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/01/2018] [Indexed: 06/10/2023]
Abstract
The green microalga Botryococcus braunii Showa, which produces large amounts of triterpene hydrocarbons, exclusively uses the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosyntheses, and the terminal enzyme in this pathway, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), is regarded as a light-dependent key regulatory enzyme. In order to investigate the possible association of HDR and ferredoxin in this organism, we constructed tertiary structure models of B. braunii HDR (BbHDR) and one of ferredoxin families in the alga, a photosynthetic electron transport F (BbPETF)-like protein, by using counterparts from E. coli and Chlamydomonas reinhardtii as templates, respectively, and performed docking analysis of these two proteins. After docked models are superimposed onto their counterpart proteins in a non-photosynthetic organism, Plasmodium falciparum, the BbPETF-like protein comes in contact with the backside of BbHDR, which was defined in a previous report (Rekittke et al. 2013), and the distance of the two Fe-S centers is 14.7 Å. This distance is in almost the same level as that for P. falicarum, 12.6 Å. To our knowledge, this is the first model suggesting the possible association of HDR with a ferredoxin in O2-evolving photosynthetic organisms.
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Affiliation(s)
- Hidenobu Uchida
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan
- Japan Science and Technology Agency-Core Research for Evolutional Science and Technology (CREST), Gobancho, Chiyoda, Tokyo 102-0076, Japan
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11
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Englund E, Shabestary K, Hudson EP, Lindberg P. Systematic overexpression study to find target enzymes enhancing production of terpenes in Synechocystis PCC 6803, using isoprene as a model compound. Metab Eng 2018; 49:164-177. [PMID: 30025762 DOI: 10.1016/j.ymben.2018.07.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/28/2018] [Accepted: 07/08/2018] [Indexed: 11/25/2022]
Abstract
Of the two natural metabolic pathways for making terpenoids, biotechnological utilization of the mevalonate (MVA) pathway has enabled commercial production of valuable compounds, while the more recently discovered but stoichiometrically more efficient methylerythritol phosphate (MEP) pathway is underdeveloped. We conducted a study on the overexpression of each enzyme in the MEP pathway in the unicellular cyanobacterium Synechocystis sp. PCC 6803, to identify potential targets for increasing flux towards terpenoid production, using isoprene as a reporter molecule. Results showed that the enzymes Ipi, Dxs and IspD had the biggest impact on isoprene production. By combining and creating operons out of those genes, isoprene production was increased 2-fold compared to the base strain. A genome-scale model was used to identify targets upstream of the MEP pathway that could redirect flux towards terpenoids. A total of ten reactions from the Calvin-Benson-Bassham cycle, lower glycolysis and co-factor synthesis pathways were probed for their effect on isoprene synthesis by co-expressing them with the MEP enzymes, resulting in a 60% increase in production from the best strain. Lastly, we studied two isoprene synthases with the highest reported catalytic rates. Only by expressing them together with Dxs and Ipi could we get stable strains that produced 2.8 mg/g isoprene per dry cell weight, a 40-fold improvement compared to the initial strain.
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Affiliation(s)
- Elias Englund
- Department of Chemistry - Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden; School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Kiyan Shabestary
- School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Elton P Hudson
- School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Pia Lindberg
- Department of Chemistry - Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
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12
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Characterization of 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (IspG) from Plasmodium vivax and it’s potential as an antimalarial drug target. Int J Biol Macromol 2017; 96:466-473. [DOI: 10.1016/j.ijbiomac.2016.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 11/15/2022]
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13
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Atkinson JT, Campbell I, Bennett GN, Silberg JJ. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. Biochemistry 2016; 55:7047-7064. [DOI: 10.1021/acs.biochem.6b00831] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, MS-180, 6100 Main Street, Houston, Texas 77005, United States
| | - Ian Campbell
- Biochemistry
and Cell Biology Graduate Program, Rice University, MS-140, 6100
Main Street, Houston, Texas 77005, United States
| | - George N. Bennett
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemical and Biomolecular Engineering, Rice University, MS-362,
6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
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14
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Kirby J, Dietzel KL, Wichmann G, Chan R, Antipov E, Moss N, Baidoo EEK, Jackson P, Gaucher SP, Gottlieb S, LaBarge J, Mahatdejkul T, Hawkins KM, Muley S, Newman JD, Liu P, Keasling JD, Zhao L. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae. Metab Eng 2016; 38:494-503. [PMID: 27989805 DOI: 10.1016/j.ymben.2016.10.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/19/2016] [Accepted: 10/25/2016] [Indexed: 01/28/2023]
Abstract
Isoprenoids are used in many commercial applications and much work has gone into engineering microbial hosts for their production. Isoprenoids are produced either from acetyl-CoA via the mevalonate pathway or from pyruvate and glyceraldehyde 3-phosphate via the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway. Saccharomyces cerevisiae exclusively utilizes the mevalonate pathway to synthesize native isoprenoids and in fact the alternative DXP pathway has never been found or successfully reconstructed in the eukaryotic cytosol. There are, however, several advantages to isoprenoid synthesis via the DXP pathway, such as a higher theoretical yield, and it has long been a goal to transplant the pathway into yeast. In this work, we investigate and address barriers to DXP pathway functionality in S. cerevisiae using a combination of synthetic biology, biochemistry and metabolomics. We report, for the first time, functional expression of the DXP pathway in S. cerevisiae. Under low aeration conditions, an engineered strain relying solely on the DXP pathway for isoprenoid biosynthesis achieved an endpoint biomass 80% of that of the same strain using the mevalonate pathway.
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Affiliation(s)
- James Kirby
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kevin L Dietzel
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Gale Wichmann
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Rossana Chan
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Eugene Antipov
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Nathan Moss
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | | | - Peter Jackson
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sara P Gaucher
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Shayin Gottlieb
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jeremy LaBarge
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Tina Mahatdejkul
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Kristy M Hawkins
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Sheela Muley
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Jack D Newman
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94702, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94702, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970 Hørsholm, Denmark
| | - Lishan Zhao
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, CA 94608, USA.
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15
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Yang C, Gao X, Jiang Y, Sun B, Gao F, Yang S. Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli. Metab Eng 2016; 37:79-91. [DOI: 10.1016/j.ymben.2016.05.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/21/2016] [Accepted: 05/05/2016] [Indexed: 01/08/2023]
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16
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Davies FK, Jinkerson RE, Posewitz MC. Toward a photosynthetic microbial platform for terpenoid engineering. PHOTOSYNTHESIS RESEARCH 2015; 123:265-84. [PMID: 24510550 DOI: 10.1007/s11120-014-9979-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/23/2014] [Indexed: 05/20/2023]
Abstract
Plant terpenoids are among the most diverse group of naturally-occurring organic compounds known, and several are used in contemporary consumer products. Terpene synthase enzymes catalyze complex rearrangements of carbon skeleton precursors to yield thousands of unique chemical structures that range in size from the simplest five carbon isoprene unit to the long polymers of rubber. Such chemical diversity has established plant terpenoids as valuable commodity chemicals with applications in the pharmaceutical, neutraceutical, cosmetic, and food industries. More recently, terpenoids have received attention as a renewable alternative to petroleum-derived fuels and as the building blocks of synthetic biopolymers. However, the current plant- and petrochemical-based supplies of commodity terpenoids have major limitations. Photosynthetic microorganisms provide an opportunity to generate terpenoids in a renewable manner, employing a single consolidated host organism that is able to use solar energy, H2O and CO2 as the primary inputs for terpenoid biosynthesis. Advances in synthetic biology have seen important breakthroughs in microbial terpenoid engineering, traditionally via fermentative pathways in yeast and Escherichia coli. This review draws on the knowledge obtained from heterotrophic microbial engineering to propose strategies for the development of microbial photosynthetic platforms for industrial terpenoid production. The importance of utilizing the wealth of genetic information provided by nature to unravel the regulatory mechanisms of terpenoid biosynthesis is highlighted.
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Affiliation(s)
- Fiona K Davies
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, 80401, USA,
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17
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Pattanaik B, Lindberg P. Terpenoids and their biosynthesis in cyanobacteria. Life (Basel) 2015; 5:269-93. [PMID: 25615610 PMCID: PMC4390852 DOI: 10.3390/life5010269] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/14/2015] [Indexed: 12/21/2022] Open
Abstract
Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the MEP pathway are the isomeric five-carbon compounds isopentenyl diphosphate and dimethylallyl diphosphate, which in turn form the basic building blocks for formation of all terpenoids. Many terpenoid compounds have useful properties and are of interest in the fields of pharmaceuticals and nutrition, and even potentially as future biofuels. The MEP pathway, its function and regulation, and the subsequent formation of terpenoids have not been fully elucidated in cyanobacteria, despite its relevance for biotechnological applications. In this review, we summarize the present knowledge about cyanobacterial terpenoid biosynthesis, both regarding the native metabolism and regarding metabolic engineering of cyanobacteria for heterologous production of non-native terpenoids.
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Affiliation(s)
- Bagmi Pattanaik
- Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
| | - Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
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18
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19
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Frohnecke N, Klein S, Seeber F. Protein-protein interaction studies provide evidence for electron transfer from ferredoxin to lipoic acid synthase in Toxoplasma gondii. FEBS Lett 2014; 589:31-6. [PMID: 25433292 DOI: 10.1016/j.febslet.2014.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 01/08/2023]
Abstract
The only known redox system in the apicoplast, a plastid-like organelle of apicomplexan parasites, is ferredoxin and ferredoxin-associated reductase. Ferredoxin donates electrons to different enzymes, presumably including lipoate synthase (LipA), which is essential for fatty acid biosynthesis. We recombinantly expressed and characterized LipA from the protozoan parasite Toxoplasma gondii, generated LipA-specific antibodies and confirmed the apicoplast localization of LipA. Electron transfer from ferredoxin to LipA would require direct protein-protein interaction. Such a robust interaction between the two proteins was demonstrated in both yeast and bacterial two-hybrid systems. Taken together, our results provide strong evidence for a role of ferredoxin as an electron donor to LipA.
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Affiliation(s)
- Nora Frohnecke
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany
| | - Sandra Klein
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany
| | - Frank Seeber
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany.
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20
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Genetically engineering cyanobacteria to convert CO2, water, and light into the long-chain hydrocarbon farnesene. Appl Microbiol Biotechnol 2014; 98:9869-77. [DOI: 10.1007/s00253-014-6118-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 01/05/2023]
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21
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Cloning and Characterization of the 2-C-Methyl-D-erythritol 4-Phosphate (MEP) Pathway Genes of a Natural-Rubber Producing Plant,Hevea brasiliensis. Biosci Biotechnol Biochem 2014; 72:2903-17. [DOI: 10.1271/bbb.80387] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Englund E, Pattanaik B, Ubhayasekera SJK, Stensjö K, Bergquist J, Lindberg P. Production of squalene in Synechocystis sp. PCC 6803. PLoS One 2014; 9:e90270. [PMID: 24625633 PMCID: PMC3953072 DOI: 10.1371/journal.pone.0090270] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/26/2014] [Indexed: 12/22/2022] Open
Abstract
In recent years, there has been an increased interest in the research and development of sustainable alternatives to fossil fuels. Using photosynthetic microorganisms to produce such alternatives is advantageous, since they can achieve direct conversion of carbon dioxide from the atmosphere into the desired product, using sunlight as the energy source. Squalene is a naturally occurring 30-carbon isoprenoid, which has commercial use in cosmetics and in vaccines. If it could be produced sustainably on a large scale, it could also be used instead of petroleum as a raw material for fuels and as feedstock for the chemical industry. The unicellular cyanobacterium Synechocystis PCC 6803 possesses a gene, slr2089, predicted to encode squalene hopene cyclase (Shc), an enzyme converting squalene into hopene, the substrate for forming hopanoids. Through inactivation of slr2089 (shc), we explored the possibility to produce squalene using cyanobacteria. The inactivation led to accumulation of squalene, to a level over 70 times higher than in wild type cells, reaching 0.67 mg OD750−1 L−1. We did not observe any significant growth deficiency in the Δshc strain compared to the wild type Synechocystis, even at high light conditions, suggesting that the observed squalene accumulation was not detrimental to growth, and that formation of hopene by Shc is not crucial for growth under normal conditions, nor for high-light stress tolerance. Effects of different light intensities and growth stages on squalene accumulation in the Δshc strain were investigated. We also identified a gene, sll0513, as a putative squalene synthase in Synechocystis, and verified its function by inactivation. In this work, we show that it is possible to use the cyanobacterium Synechocystis to generate squalene, a hydrocarbon of commercial interest and a potential biofuel. We also report the first identification of a squalene hopene cyclase, and the second identification of squalene synthase, in cyanobacteria.
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Affiliation(s)
- Elias Englund
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bagmi Pattanaik
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry, BMC and Science for Life Laboratory, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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24
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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25
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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26
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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27
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Li Z, Sharkey TD. Metabolic profiling of the methylerythritol phosphate pathway reveals the source of post-illumination isoprene burst from leaves. PLANT, CELL & ENVIRONMENT 2013; 36:429-37. [PMID: 22831282 DOI: 10.1111/j.1365-3040.2012.02584.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The methylerythritol phosphate (MEP) pathway in plants produces the prenyl precursors for all plastidic isoprenoids, including carotenoids and quinones. The MEP pathway is also responsible for synthesis of approximately 600 Tg of isoprene per year, the largest non-methane hydrocarbon flux into the atmosphere. There have been few studies of the regulation of the MEP pathway in plants under physiological conditions. In this study, we combined gas exchange techniques and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) and measured the profile of MEP pathway metabolites under different conditions. We report that in the MEP pathway, metabolites immediately preceding steps requiring reducing power were in high concentration. Inhibition of the MEP pathway by fosmidomycin caused deoxyxylulose phosphate accumulation in leaves as expected. Evidence is presented that accumulation of MEP pathway intermediates, primarily methylerythritol cyclodiphosphate, is responsible for the post-illumination isoprene burst phenomenon. Pools of intermediate metabolites stayed at approximately the same level 10 min after light was turned off, but declined eventually under prolonged darkness. In contrast, a strong inhibition of the second-to-last step of the MEP pathway caused suppression of isoprene emission in pure N(2). Our study suggests that reducing equivalents may be a key regulator of the MEP pathway and therefore isoprene emission from leaves.
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Affiliation(s)
- Ziru Li
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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28
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Machado IM, Atsumi S. Cyanobacterial biofuel production. J Biotechnol 2012; 162:50-6. [DOI: 10.1016/j.jbiotec.2012.03.005] [Citation(s) in RCA: 209] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/28/2012] [Accepted: 03/08/2012] [Indexed: 12/31/2022]
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Structure, function and inhibition of the two- and three-domain 4Fe-4S IspG proteins. Proc Natl Acad Sci U S A 2012; 109:8558-63. [PMID: 22586085 DOI: 10.1073/pnas.1121107109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
IspG is a 4Fe4S protein involved in isoprenoid biosynthesis. Most bacterial IspGs contain two domains: a TIM barrel (A) and a 4Fe4S domain (B), but in plants and malaria parasites, there is a large insert domain (A*) whose structure and function are unknown. We show that bacterial IspGs function in solution as (AB)(2) dimers and that mutations in either both A or both B domains block activity. Chimeras harboring an A-mutation in one chain and a B-mutation in the other have 50% of the activity seen in wild-type protein, because there is still one catalytically active AB domain. However, a plant IspG functions as an AA*B monomer. We propose, using computational modeling and electron microscopy, that the A* insert domain has a TIM barrel structure that interacts with the A domain. This structural arrangement enables the A and B domains to interact in a "cup and ball" manner during catalysis, just as in the bacterial systems. EPR/HYSCORE spectra of reaction intermediate, product, and inhibitor ligands bound to both two and three domain proteins are identical, indicating the same local electronic structure, and computational docking indicates these ligands bridge both A and B domains. Overall, the results are of broad general interest because they indicate the insert domain in three-domain IspGs is a second TIM barrel that plays a structural role and that the pattern of inhibition of both two and three domain proteins are the same, results that can be expected to be of use in drug design.
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30
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Catalano-Dupuy DL, Musumeci MA, López-Rivero A, Ceccarelli EA. A highly stable plastidic-type ferredoxin-NADP(H) reductase in the pathogenic bacterium Leptospira interrogans. PLoS One 2011; 6:e26736. [PMID: 22039544 PMCID: PMC3200346 DOI: 10.1371/journal.pone.0026736] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 10/03/2011] [Indexed: 01/18/2023] Open
Abstract
Leptospira interrogans is a bacterium that is capable of infecting animals and humans, and its infection causes leptospirosis with a range of symptoms from flu-like to severe illness and death. Despite being a bacteria, Leptospira interrogans contains a plastidic class ferredoxin-NADP(H) reductase (FNR) with high catalytic efficiency, at difference from the bacterial class FNRs. These flavoenzymes catalyze the electron transfer between NADP(H) and ferredoxins or flavodoxins. The inclusion of a plastidic FNR in Leptospira metabolism and in its parasitic life cycle is not currently understood. Bioinformatic analyses of the available genomic and proteins sequences showed that the presence of this enzyme in nonphotosynthetic bacteria is restricted to the Leptospira genus and that a [4Fe-4S] ferredoxin (LB107) encoded by the Leptospira genome may be the natural substrate of the enzyme. Leptospira FNR (LepFNR) displayed high diaphorase activity using artificial acceptors and functioned as a ferric reductase. LepFNR displayed cytochrome c reductase activity with the Leptospira LB107 ferredoxin with an optimum at pH 6.5. Structural stability analysis demonstrates that LepFNR is one of the most stable FNRs analyzed to date. The persistence of a native folded LepFNR structure was detected in up to 6 M urea, a condition in which the enzyme retains 38% activity. In silico analysis indicates that the high LepFNR stability might be due to robust interactions between the FAD and the NADP+ domains of the protein. The limited bacterial distribution of plastidic class FNRs and the biochemical and structural properties of LepFNR emphasize the uniqueness of this enzyme in the Leptospira metabolism. Our studies show that in L. interrogans a plastidic-type FNR exchanges electrons with a bacterial-type ferredoxin, process which has not been previously observed in nature.
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Affiliation(s)
- Daniela L Catalano-Dupuy
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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31
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Xiao Y, Rooker D, You Q, Meyers CLF, Liu P. IspG-catalyzed positional isotopic exchange in methylerythritol cyclodiphosphate of the deoxyxylulose phosphate pathway: mechanistic implications. Chembiochem 2011; 12:527-30. [PMID: 22238143 DOI: 10.1002/cbic.201000716] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 11/07/2022]
Abstract
H(2)(18)O under the bridge: Recently, the deoxyxylulose phosphate (DXP) pathway was discovered to be a second pathway supplying isoprenoid biosynthetic precursors. One of steps is an IspG-catalyzed reductive deoxygenation of methylerythritol cyclodiphosphate (MEcPP) to 4-hydroxyl-3-methyl-2-(E)-1-diphosphate (HMBPP). Using [2-(13) C,(18) O]-MEcPP, we detected the positional isotopic exchange for the bridging oxygen in MEcPP.
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Affiliation(s)
- Youli Xiao
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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32
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Gräwert T, Span I, Bacher A, Groll M. Reduktive Dehydroxylierung von Allylalkoholen durch IspH-Protein. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Gräwert T, Span I, Bacher A, Groll M. Reductive Dehydroxylation of Allyl Alcohols by IspH Protein. Angew Chem Int Ed Engl 2010; 49:8802-9. [DOI: 10.1002/anie.201000833] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Xu W, Lees NS, Adedeji D, Wiesner J, Jomaa H, Hoffman BM, Duin EC. Paramagnetic Intermediates of (E)-4-Hydroxy-3-methylbut-2-enyl Diphosphate Synthase (GcpE/IspG) under Steady-State and Pre-Steady-State Conditions. J Am Chem Soc 2010; 132:14509-20. [DOI: 10.1021/ja101764w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weiya Xu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Nicholas S. Lees
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Dolapo Adedeji
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Jochen Wiesner
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Hassan Jomaa
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Brian M. Hoffman
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Evert C. Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
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35
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Xiao Y, Nyland RL, Meyers CLF, Liu P. Methylerythritol cyclodiphosphate (MEcPP) in deoxyxylulose phosphate pathway: synthesis from an epoxide and mechanisms. Chem Commun (Camb) 2010; 46:7220-2. [PMID: 20820543 DOI: 10.1039/c0cc02594a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this communication, we reported another unique IspG-catalyzed transformation, the production of its substrate, MEcPP, from (2R,3R)-4-hydroxy-3-methyl-2,3-epoxybutanyl diphosphate (Epoxy-HMBPP) when reductants are excluded from the reaction mixture.
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Affiliation(s)
- Youli Xiao
- Department of Chemistry, Boston University, MA 02215, USA
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36
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Seeber F, Soldati-Favre D. Metabolic Pathways in the Apicoplast of Apicomplexa. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 281:161-228. [DOI: 10.1016/s1937-6448(10)81005-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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37
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PetH is rate-controlling in the interaction between PetH, a component of the supramolecular complex with photosystem II, and PetF, a light-dependent electron transfer protein. Biochem Biophys Res Commun 2009; 389:394-8. [PMID: 19733549 DOI: 10.1016/j.bbrc.2009.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 09/01/2009] [Indexed: 11/23/2022]
Abstract
Cyanobacterial PetH is similar to ferredoxin-NADP(+) oxidoreductase (FNR) of higher plants and comprises 2 components, CpcD-like rod linker and FNR proteins. Here, I show that PetH controls the rate of the interaction with PetF (ferredoxin [Fd1]). Purified recombinant PetH protein, which cut off a CpcD-like rod linker domain, and Fd1 were used in detailed surface plasmon resonance analyses. The interaction between FNR and Fd1 chiefly involved extremely fast binding and dissociation reactions and the FNR affinity for Fd1 was stronger than the Fd1 affinity for FNR. The dissociation constant values were determined as approximately 93.65 microM (FNR) for Fd1 and 1.469 mM (Fd1) for FNR.
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38
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Jones MB, Rosenberg JN, Betenbaugh MJ, Krag SS. Structure and synthesis of polyisoprenoids used in N-glycosylation across the three domains of life. Biochim Biophys Acta Gen Subj 2009; 1790:485-94. [PMID: 19348869 DOI: 10.1016/j.bbagen.2009.03.030] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/26/2009] [Accepted: 03/30/2009] [Indexed: 01/11/2023]
Abstract
N-linked protein glycosylation was originally thought to be specific to eukaryotes, but evidence of this post-translational modification has now been discovered across all domains of life: Eucarya, Bacteria, and Archaea. In all cases, the glycans are first assembled in a step-wise manner on a polyisoprenoid carrier lipid. At some stage of lipid-linked oligosaccharide synthesis, the glycan is flipped across a membrane. Subsequently, the completed glycan is transferred to specific asparagine residues on the protein of interest. Interestingly, though the N-glycosylation pathway seems to be conserved, the biosynthetic pathways of the polyisoprenoid carriers, the specific structures of the carriers, and the glycan residues added to the carriers vary widely. In this review we will elucidate how organisms in each basic domain of life synthesize the polyisoprenoids that they utilize for N-linked glycosylation and briefly discuss the subsequent modifications of the lipid to generate a lipid-linked oligosaccharide.
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Affiliation(s)
- Meredith B Jones
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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39
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Okada K. HO1 and PcyA proteins involved in phycobilin biosynthesis form a 1:2 complex with ferredoxin-1 required for photosynthesis. FEBS Lett 2009; 583:1251-6. [DOI: 10.1016/j.febslet.2009.03.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 03/18/2009] [Accepted: 03/23/2009] [Indexed: 10/21/2022]
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40
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Okada K. The novel heme oxygenase-like protein fromPlasmodiumfalciparumconverts heme to bilirubin IXα in the apicoplast. FEBS Lett 2008; 583:313-9. [DOI: 10.1016/j.febslet.2008.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 12/02/2008] [Accepted: 12/05/2008] [Indexed: 11/24/2022]
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41
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From molecular fossils of bacterial hopanoids to the formation of isoprene units: discovery and elucidation of the methylerythritol phosphate pathway. Lipids 2008; 43:1095-107. [PMID: 19011917 DOI: 10.1007/s11745-008-3261-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
Investigations on the biosynthesis of bacterial triterpenoids of the hopane series led to the unexpected discovery of an alternative mevalonate independent pathway for the formation of isoprene units. Methylerythritol phosphate, already presenting the C5 branched isoprene skeleton, is the key intermediate. This pathway was independently characterized in ginkgo embryos for the formation of diterpenoids. It is present in most bacteria and in the plastids of all organisms belonging to phototrophic phyla. The key steps of the discovery and elucidation of this metabolic route are presented in this review.
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42
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Cloning, solubilization, and characterization of squalene synthase from Thermosynechococcus elongatus BP-1. J Bacteriol 2008; 190:3808-16. [PMID: 18375558 DOI: 10.1128/jb.01939-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Squalene synthase (SQS) is a bifunctional enzyme that catalyzes the condensation of two molecules of farnesyl diphosphate (FPP) to give presqualene diphosphate (PSPP) and the subsequent rearrangement of PSPP to squalene. These reactions constitute the first pathway-specific steps in hopane biosynthesis in Bacteria and sterol biosynthesis in Eukarya. The genes encoding SQS were isolated from the hopane-producing bacteria Thermosynechococcus elongatus BP-1, Bradyrhizobium japonicum, and Zymomonas mobilis and cloned into an Escherichia coli expression system. The expressed proteins with a His(6) tag were found exclusively in inclusion bodies when no additives were used in the buffer. After extensive optimization, soluble recombinant T. elongatus BP-1 SQS was obtained when cells were disrupted and purified in buffers containing glycerol. The recombinant B. japonicum and Z. mobilis SQSs could not be solubilized under any of the expression and purification conditions used. Purified T. elongatus His(6)-SQS gave a single band at 42 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and molecular ion at m/z 41886 by electrospray mass spectrometry. Incubation with FPP and NADPH gave squalene as the sole product. Incubation of the enzyme with [(14)C]FPP in the absence of NADPH gave PSPP. The enzyme requires Mg(2+) for activity, has an optimum pH of 7.6, and is strongly stimulated by detergent. Under optimal conditions, the K(m) of FPP is 0.97 +/- 0.10 microM and the k(cat) is 1.74 +/- 0.04 s(-1). Zaragozic acid A, a potent inhibitor of mammalian, fungal, and Saccharomyces cerevisiae SQSs, also inhibited recombinant T. elongatus BP-1 SQS, with a 50% inhibitory concentration of 95.5 +/- 13.6 nM.
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43
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Yamamoto H, Nomata J, Fuita Y. Functional expression of nitrogenase-like protochlorophyllide reductase from Rhodobacter capsulatus in Escherichia coli. Photochem Photobiol Sci 2008; 7:1238-42. [DOI: 10.1039/b802427h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Ershov YV. 2-C-methylerythritol phosphate pathway of isoprenoid biosynthesis as a target in identifying new antibiotics, herbicides, and immunomodulators: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807020019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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45
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Rohmer M. Diversity in isoprene unit biosynthesis: The methylerythritol phosphate pathway in bacteria and plastids. PURE APPL CHEM 2007. [DOI: 10.1351/pac200779040739] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The long-overlooked methylerythritol phosphate (MEP) pathway represents an alternative to the mevalonate route for the formation of isoprene units. It is found in most bacteria as well as in the plastids of all phototrophic organisms. A selection of significant steps of its discovery and elucidation are presented in this contribution, as well as a complete hypothetical biogenetic scheme for the last reduction step.
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Affiliation(s)
- Michel Rohmer
- 1Université Louis Pasteur/CNRS, Institut de Chemie, 4 rue Blaise Pascal, 67070 Strasbourg Cédex, France
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46
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Mahmud T. Isotope tracer investigations of natural products biosynthesis: the discovery of novel metabolic pathways. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1391] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Stelter K, El-Sayed NM, Seeber F. The Expression of a Plant-type Ferredoxin Redox System provides Molecular Evidence for a Plastid in the Early Dinoflagellate Perkinsus marinus. Protist 2007; 158:119-30. [PMID: 17123864 DOI: 10.1016/j.protis.2006.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 09/29/2006] [Indexed: 11/18/2022]
Abstract
Perkinsus marinus is a parasitic protozoan with a phylogenetic positioning between Apicomplexa and dinoflagellates. It is thus of interest for reconstructing the early evolution of eukaryotes, especially with regard to the acquisition of secondary plastids in these organisms. It is also an important pathogen of oysters, and the definition of parasite-specific metabolic pathways would be beneficial for the identification of efficient treatments for infected mollusks. Although these different scientific interests have resulted in the start of a genome project for this organism, it is still unknown whether P. marinus contains a plastid or plastid-like organelle like the related dinoflagellates and Apicomplexa. Here, we show that in vitro-cultivated parasites contain transcripts of the plant-type ferredoxin and its associated reductase. Both proteins are nuclear-encoded and possess N-terminal targeting sequences similar to those characterized in dinoflagellates. Since this redox pair is exclusively found in cyanobacteria and plastid-harboring organisms its presence also in P. marinus is highly indicative of a plastid. We also provide additional evidence for such an organelle by demonstrating pharmacological sensitivity to inhibitors of plastid-localized enzymes involved in fatty acid biosynthesis (e.g. acetyl-CoA carboxylase) and by detection of genes for three enzymes of plastid-localized isoprenoid biosynthesis (1-deoxy-D-xylulose 5-phosphate reductoisomerase, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, and (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase).
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Affiliation(s)
- Kathrin Stelter
- FB Biologie/Parasitologie, Philipps-Universität Marburg, 35032 Marburg, Germany
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48
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Adedeji D, Hernandez H, Wiesner J, Köhler U, Jomaa H, Duin EC. Possible direct involvement of the active-site [4Fe-4S] cluster of the GcpE enzyme fromThermus thermophilusin the conversion of MEcPP. FEBS Lett 2006; 581:279-83. [PMID: 17214985 DOI: 10.1016/j.febslet.2006.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/05/2006] [Accepted: 12/08/2006] [Indexed: 11/15/2022]
Abstract
The GcpE enzyme converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) in the penultimate step of the DOXP pathway for isoprene biosynthesis. Purification of the enzyme under exclusion of air leads to a preparation that contains solely [4Fe-4S] clusters. Kinetic studies showed that in the presence of the artificial reductant dithionite and MEcPP a new transient iron-sulfur-based signal is detected in electron paramagnetic resonance (EPR) spectroscopy. Similarity of this EPR signal to that detected in ferredoxin:thioredoxin reductase indicates that during the reaction an intermediate is directly bound to the active-site cluster.
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Affiliation(s)
- Dolapo Adedeji
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849, USA
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49
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Röhrich RC, Englert N, Troschke K, Reichenberg A, Hintz M, Seeber F, Balconi E, Aliverti A, Zanetti G, Köhler U, Pfeiffer M, Beck E, Jomaa H, Wiesner J. Reconstitution of an apicoplast-localised electron transfer pathway involved in the isoprenoid biosynthesis of Plasmodium falciparum. FEBS Lett 2005; 579:6433-8. [PMID: 16289098 DOI: 10.1016/j.febslet.2005.10.037] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 10/18/2005] [Accepted: 10/19/2005] [Indexed: 11/20/2022]
Abstract
In the malaria parasite Plasmodium falciparum isoprenoid precursors are synthesised inside a plastid-like organelle (apicoplast) by the mevalonate independent 1-deoxy-d-xylulose-5-phosphate (DOXP) pathway. The last reaction step of the DOXP pathway is catalysed by the LytB enzyme which contains a [4Fe-4S] cluster. In this study, LytB of P. falciparum was shown to be catalytically active in the presence of an NADPH dependent electron transfer system comprising ferredoxin and ferredoxin-NADP(+) reductase. LytB and ferredoxin were found to form a stable protein complex. These data suggest that the ferredoxin/ferredoxin-NADP(+) reductase redox system serves as the physiological electron donor for LytB in the apicoplast of P. falciparum.
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Affiliation(s)
- René C Röhrich
- Biochemisches Institut, Justus-Liebig-Universität Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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50
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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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