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(Last modification: 10. April 2010)

 

Typ III Polyketidsynthasen (PKS) in Bakterien

 

Stilbensynthase (STS) Typ Ring-Faltung

 

Alkylresorcinole in Streptomyces griseus

Schlüssel-Publikation: Funabashi et al., 2008

   RppA, eine Typ III PKS aus diesem Bakterium,  wurde bereits früher in vielen Einzelheiten charakterisiert (Funa et al., 1999; Funa et al., 2002a; Funa et al., 2002b) und ebenso ein ganz ähnliches Enzym aus Streptomyces coelicor (Izumikawa et al., 2003; Austin et al., 2004; Li et al., 2007). Die Enzyme katalysieren die Synthese von 1,3,6,8-Tetrahydroxynaphthalen (T4HN): Mehr

   Bei der Vollendung der genomischen Sequenz von Streptomyces griseus (Ohnishi et al., 2008) wurde eine weitere Typ III PKS entdeckt. Sie war Teil eines Operons namens srs (Streptomyces Resorcinol Synthese). Das Operon enthält drei Gene: srsA, die Typ III PKS, SrsB, mit Ähnlichkeiten zu Methyltransferasen, und srsC, mit Motiven, die man aus Flavoprotein-Hydroxylasen kennt.

   Bei der Analyse der Funktion wurden zunächst Teile des Operons inaktiviert, und dann die Metaboliten-Profile untersucht, nach Expression der Gene in transgenem Streptomyces lividans TK21. Die Zellen mit nur dem leeren Vektor enthielten gar keine phenolischen Komponenten. Dies war anders mit den verschiedenen Konstrukten. Sie und die Produkte sind in Fig. 1 zusammengefasst. SrsA allein führte zu Bildung von Resorcinolen mit einer Methylgruppe am Resorcinol-Ring-System. Die zusätzliche Expression von srsB resultierte in methoxylierten Produkten, und wenn dazu noch srsC exprimiert wurde, fand man Alkylchinone, die durch eine zusätzliche Hydroxylierung und Oxidation erklärt werden konnten. Die Summe dieser Daten führte zu dem Schluss, dass die Abfolge der Reaktionen so verlief wie in Fig. 1 dargestellt: Eine Polyketidsynthase (PKS) zur Synthese des Resorcinol-Grundgerüstes, danach eine O-Methyltransferase, gefolgt von einer zusätzlichen Hydroxylierung und noch einer Oxidation.

Fig. 1.

 

   Auf den ersten Blick sah die von SrsA katalysierte PKS-Reaktion sehr ähnlich aus wie die STS-Typ-Reaktionen mit langkettigen Fettsäuren, die mit anderen Typ III PKS gefunden wurden, also mit ArsB in dem Bakterium Azotobacter vinelandii (Biosynthese von langkettigen Alkylresorcinolen, die in den Cysten deponiert werden: Mehr…), oder bei der Biosynthese von Sorgoleone in der Hirse (Sorghum bicolor (L.) Moench) (Mehr...). Weiter unten sind noch andere Beispiele für Typ III PKS, die präferentiell mit langkettigen Fettsäuren arbeiten: Mehr...

   Es gab jedoch einen auffallenden Unterschied zu typischen STS-Reaktionen: Das SrsA Produkt enthielt eine Methylgruppe an dem neu synthetisierten aromatischen Ringsystem (s. Fig. 1). Das musste erklärt werden, denn die Standard-STS-Typ Reaktion mit Malonyl-CoA führt keine C-Methylgruppe in den Resorcinol-Ring ein.

   Dies wurde mit rekombinantem SrsA untersucht. Da die Expression in E. coli nicht so gut klappte, wurde das Enzym in Streptomyces lividans produziert. Die Ergebnisse waren ganz interessant; sie sind in Fig. 2 zusammengefasst. Inkubation des Proteins nur mit Malonyl-CoA ergab überhaupt kein Produkt. Wenn nur Methylmalonyl-CoA eingesetzt wurde, erhielt man ein dimethyliertes Triketid-Pyron, welches sich einfach aus zwei Kondensationen mit Methylmalonyl-CoA erklären lässt. Das in vivo identifizierte Produkt erhielt man nur dann, wenn sowohl Malonyl-CoA als auch Methylmalonyl-CoA in dem Enzymtest vorhanden waren. Die Ergebnisse zeigten also, dass SrsA die beiden Kettenverlängerer in einer strikt kontrollierten Reihenfolge verwendete! Unglücklicherweise brachten die Autoren in der Original-Publikation die Reihenfolge durcheinander, aber das wurde in einem Erratum korrigiert (siehe unten): Die Reihenfolge der Kondensationen muss sein: Methylmalonyl-CoA, Malonyl-CoA, und noch einmal Malonyl-CoA, wie in Fig. 2 dargestellt.

Fig. 2.
R = langkettige Acyl-CoA Ester. Die Farben kennzeichnen die Kettenverlänger in der Reaktions-Sequenz.

 

   Dies waren wirklich aufregende Ergebnisse: Sie sind einzigartig, als das erste überzeugende Beispiel, dass eine Typ III PKS diese beiden Kettenverlängerer in einer genau kontrollierten Abfolge verwendet. Und das Schöne daran ist, dass die Produkte auch einer physiologischen Rolle zugeordnet werden konnten. Diese Alkyresorcinole haben vermutlich eine wichtige Rolle für die Zellwand: Sie sind ein wichtiger Teil der Resistenz der Bakterien gegen Penicillin. Und noch etwas: Die Suchen der Autoren in anderen Genomen zeigten, dass viele anderen Bakterien zu srs eng verwandte Operone enthalten; das Supplement zu der Funabashi et al. (2008) Publikation enthält eine lange und interessante Liste dafür. Es sieht so aus, als ob solche Alkylresorcinole oder verwandte Substanzen viel verbreiteter sind als bisher vermutet.

Eine interessante Frage ist, ob dieses Enzym wohl den "aldol switch mechanism" verwendet, der mit der Stilbensynthase (STS) aus der Kiefer (Pinus sylvestris) entdeckt wurde: Mehr...

   Das einzige andere Beispiel für die Verwendung verschiedener Kettenverlängerer scheint die Curcuminoid-Synthase zu sein, die aus Reis (Oryza sativa) kloniert wurde: Sie verwendet einen Phenylpropanoid-CoA Ester als Starter-Substrat, bildet mit Malonyl-CoA ein Diketid, und verwendet dieses Diketid als Kettenverlängerer in einer weiteren Kondensation mit 4-Coumaroyl-CoA als Substrat: Mehr. Hochinteressant, wenn auch mit dem kleinen Schönheitsfehler, dass Curcuminoide in Reis noch nie gefunden wurden.

   Es sollte hinzugefügt werden, dass die Verwendung von Methylmalonyl-CoA durch Typ III PKS nichts Ungewöhnliches oder Neues ist. so etwas wurde bereits vor langer Zeit mit einem Enzym aus der Kiefer (Pinus sylvestris) gezeigt; dieses Protein könnte an der Biosynthese von methylierten Chalcon-Derivaten beteiligt sein: Mehr…Andere Arbeiten lassen vermuten, dass Typ III PKS generell in der Lage sind, Methylmalonyl-CoA als Kettenverlängerer zu akzeptieren  (Abe et al., 2002; Abe et al., 2003; Abe et al., 2006). Dies scheint jedoch in der Regel eine reine in vitro Aktivität darzustellen, denn sie führt nicht zu Produkten, die aus den Pflanzen bekannt sind.

 

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Andere Typ III PKS mit Substrat-Präferenzen für langkettige CoA-Estern in Pflanzen und in Bakterien

  • Alkylpyrone und Alkylresorcinole in dem Moos Physcomitrella patens: Mehr...

  • Sorgoleone Biosynthese in der Hirse Sorghum bicolor : Mehr...

  • Pyronbiosynthese in A. thaliana: Mehr...

  • Alkylresorcinole und langkettige Pyrone in dem Bakterium Azotobacter vinelandii: Mehr...

  • Diese Seite: Alkylresorcinol-Biosynthese in dem Bakterium Streptomyces griseus: Mehr...         

  • Pyronsynthasen in dem Bakterium Mycobacterium tuberculosis und Bacillus subtilis: Mehr...

  • CsyA: Pyronsynthasen in dem Pilz Aspergillus oryzae: Mehr...

  


 

Links zu bakteriellen Typ III PKS

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  • Funabashi, M., Funa, N., Horinouchi, S., 2008. Phenolic lipids synthesized by type III polyketide synthase confer penicillin resistance on Streptomyces griseus. Journal of Biological Chemistry 283, 13983-13991.
    Type III polyketide synthases (PKSs) found in plants, fungi, and bacteria synthesize a variety of aromatic polyketides. A Gram-positive, filamentous bacterium Streptomyces griseus contained an srs operon, in which srsA encoded a type III PKS, srsB encoded a methyltransferase, and srsC encoded a flavoprotein hydroxylase. Consistent with this annotation, overexpression of the srs genes in a heterologous host, Streptomyces lividans, showed that SrsA was a type III PKS responsible for synthesis of phenolic lipids, alkylresorcinols, and alkylpyrones, SrsB was a methyltransferase acting on the phenolic lipids to yield alkylresorcinol methyl ethers, and SrsC was a hydroxylase acting on the alkylresorcinol methyl ethers. In vitro SrsA reaction showed that SrsA synthesized alkylresorcinols from acyl-CoAs of various chain lengths as a starter substrate, one molecule of methylmalonyl-CoA, and two molecules of malonyl-CoA. SrsA was thus unique in that it incorporated the extender substrates in a strictly controlled order of malonyl-CoA, malonyl-CoA, and methylmalonyl-CoA (see erratum below) to produce alkylresorcinols. An srsA mutant, which produced no phenolic lipids, was highly sensitive to beta-lactam antibiotics, such as penicillin G and cephalexin. Together with the fact that the alkylresorcinols were fractionated mainly in the cell wall fraction, this observation suggests that the phenolic lipids, perhaps associated with the cytoplasmic membrane because of their amphiphilic property, affect the characteristic and rigidity of the cytoplasmic membrane/peptidoglycan of a variety of bacteria. An srs-like operon is found widely among Gram-positive and -negative bacteria, indicating wide distribution of the phenolic lipids.
    Protein accession:
    YP_001821984
    Zum Seitenanfang
    Erratum in: J. Biol. Chem. 2008 Sep 5; Vol. 283, page 25104.
    On Page 13990, the mode of ring folding of the tetraketide intermediate, leading to resorcinol formation, in Fig. 5B was incorrect. The correct ring folding is C-2-C-7 aldol condensation. This error does not change the conclusions of this study. However, the order of condensation of the extender units is updated as methylmalonyl-CoA, malonyl-CoA, and malonyl-CoA.
    Zurück zum Text

  • Ohnishi, Y., Ishikawa, J., Hara, H., Suzuki, H., Ikenoya, M., Ikeda, H., Yamashita, A., Hattori, M., Horinouchi, S., 2008. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. Journal of Bacteriology 190, 4050-4060.
      
    We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are different from those of typical telomeres conserved among other Streptomyces species. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species, Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone signaling molecule) regulatory cascade in S. griseus.
    Zurück

  • Abe, I., Takahashi, Y., Lou, W., Noguchi, H., 2003. Enzymatic formation of unnatural novel polyketides from alternate starter and nonphysiological extension substrate by chalcone synthase. Organic Letters 5, 1277-1280.
      
    In the chalcone synthase (CHS) enzyme reaction, both the starter molecule and the extension unit of the poyketide chain elongation reaction were simultaneously replaced with nonphysiological substrates. When incubated with benzoyl-CoA and methylmalonyl-CoA as substrates, recombinant CHS from Scutellaria baicalensis afforded an unnatural novel triketide, 4-hydroxy-3,5-dimethyl-6-phenyl-pyran-2-one, along with a tetraketide, 4-hydroxy-3,5-dimethyl-6-(1-methyl-2-oxo-2-phenyl-ethyl)-pyran-2-one. On the other hand, the enzyme also accepted hexanoyl-CoA and methylmalonyl-CoA as substrates to produce an unnatural novel triketide, 4-hydroxy-3,5-dimethyl-6-pentyl-pyran-2-one.
    Zurück

  • Abe, I., Takahashi, Y., Noguchi, H., 2002. Enzymatic formation of an unnatural C6-C5 aromatic polyketide by plant type III polyketide synthases. Organic Letters 4, 3623-3626.
    Substrate specificities of plant polyketide synthases (PKSs) were investigated using analogues of malonyl-CoA, the extension unit of the polyketide chain elongation reactions. When incubated with methylmalonyl-CoA and 4-coumaroyl-CoA, plant PKSs (chalcone synthase from Scutellaria baicalensis, stilbene synthase from Arachis hypogaea, and benzalacetone synthase from Rheum palmatum) afforded an unnatural C(6)-C(5) aromatic polyketide, 1-(4-hydroxyphenyl)pent-1-en-3-one, formed by one-step decarboxylative condensation of the two substrates. In contrast, succinyl-CoA was not accepted as a substrate by the enzymes.
    Zurück

  • Abe, T., Noma, H., Noguchi, H., Abe, I., 2006. Enzymatic formation of an unnatural methylated triketide by plant type III polyketide synthases. Tetrahedron Letters 47, 8727-8730.
      
    Octaketide synthase, a novel plant-specific type III polyketide synthase from Aloe arborescens, efficiently accepted (2RS)-methylmalonyl-CoA as a sole substrate to produce 6-ethyl-4-hydroxy-3,5-dimethyl-2-pyrone. On the other hand, a tetraketide-producing chalcone synthase from Scutellaria baicalensis and a diketide-producing benzalacetone synthase from Rheum palmatum also yielded the unnatural methylated C9 triketide pyrone as a single product by sequential decarboxylative condensations of three molecules of (2RS)-methylmalonyl-CoA.
    Zurück

  • Austin, M. B., Izumikawa, M., Bowman, M. E., Udwary, D. W., Ferrer, J.-L., Moore, B. S., Noel, J. P., 2004. Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. Journal of Biological Chemistry 279, 45162-45174.
      
    In bacteria, a structurally simple type III polyketide synthase (PKS) known as 1,3,6,8-tetrahydroxynaphthlene synthase (THNS) catalyzes the iterative condensation of five CoA-linked malonyl units to form a pentaketide intermediate. THNS subsequently catalyzes dual intramolecular Claisen and aldol condensations of this linear intermediate to produce the fused ring tetrahydroxynaphthalene (THN) skeleton. The type III PKS-catalyzed polyketide extension mechanism, utilizing a conserved Cys-His-Asn catalytic triad in an internal active site cavity, is fairly well understood. However, the mechanistic basis for the unusual production of THN and dual cyclization of its malonyl-primed pentaketide is obscure. Here we present the first bacterial type III PKS crystal structure, that of Streptomyces coelicolor THNS, and identify by mutagenesis, structural modeling, and chemical analysis the unexpected catalytic participation of an additional THNS-conserved cysteine residue in facilitating malonyl-primed polyketide extension beyond the triketide stage. The resulting new mechanistic model, involving the use of additional cysteines to alter and steer polyketide reactivity, may generally apply to other PKS reaction mechanisms, including those catalyzed by iterative type I and II PKS enzymes. Our crystal structure also reveals an unanticipated novel cavity extending into the "floor" of the traditional active site cavity, providing the first plausible structural and mechanistic explanation for yet another unusual THNS catalytic activity: its previously inexplicable extra polyketide extension step when primed with a long acyl starter. This tunnel allows for selective expansion of available active site cavity volume by sequestration of aliphatic starter-derived polyketide tails, and further suggests another distinct protection mechanism involving maintenance of a linear polyketide conformation.
    Zurück

  • Funa, N., Ohnishi, Y., Ebizuka, Y., Horinouchi, S., 2002a. Alteration of reaction and substrate specificity of a bacterial type III polyketide synthase by site-directed mutagenesis. Biochemical Journal 367, 781-789.
      
    RppA, which belongs to the type III polyketide synthase family, catalyses the synthesis of 1,3,6,8-tetrahydroxynaphthalene (THN), which is the key intermediate of melanin biosynthesis in the bacterium Streptomyces griseus. The reaction of THN synthesis catalysed by RppA is unique in the type III polyketide synthase family, in that it selects malonyl-CoA as a starter substrate. The Cys-His-Asn catalytic triad is also present in RppA, as in plant chalcone synthases, as revealed by analyses of active-site mutants having amino acid replacements at Cys(138), His(270) and Asn(303) of RppA. Site-directed mutagenesis of the amino acid residues that are likely to form the active-site cavity revealed that the aromatic ring of Tyr(224) is essential for RppA to select malonyl-CoA as a starter substrate, since substitution of Tyr(224) by amino acids other than Phe and Trp abolished the ability of RppA to accept malonyl-CoA as a starter, whereas the mutant enzymes Y224F and Y224W were capable of synthesizing THN via the malonyl-CoA-primed reaction. Of the site-directed mutants generated, A305I was found to produce only a triketide pyrone from hexanoyl-CoA as starter substrate, although wild-type RppA synthesizes tetraketide and triketide pyrones in the hexanoyl-CoA-primed reaction. The kinetic parameters of Ala(305) mutants and identification of their products showed that the substitution of Ala(305) by bulky amino acid residues restricted the number of elongations of the growing polyketide chain. Both Tyr(224) (important for starter substrate selection) and Ala(305) (important for intermediate elongation) were found to be conserved in three other RppAs from Streptomyces antibioticus and Streptomyces lividans.
    Zurück

  • Funa, N., Ohnishi, Y., Ebizuka, Y., Horinouchi, S., 2002b. Properties and substrate specificity of RppA, a chalcone synthase-related polyketide synthase in Streptomyces griseus. Journal of Biological Chemistry 277, 4628-4635.
      
    RppA, a chalcone synthase-related polyketide synthase (type III polyketide synthase) in the bacterium Streptomyces griseus, catalyzes the formation of 1,3,6,8-tetrahydroxynaphthalene (THN) from five molecules of malonyl-CoA (i.e. starter malonyl-CoA + 4 condensations with malonyl-CoA). The Km value for malonyl-CoA and the kcat value for THN synthesis were determined to be 0.93 +/-  0.1 µM and 0.77 +/-  0.04 min(-1), respectively. RppA accepted aliphatic acyl-CoAs with the carbon lengths from C4 to C8 as starter substrates and catalyzed sequential condensation of malonyl-CoA to yield alpha-pyrones and phloroglucinols. In addition, RppA yielded a hexaketide, 4-hydroxy-6-(2,4,6-trioxotridecyl)-2-pyrone, from octanoyl-CoA and five molecules of malonyl-CoA, suggesting that the size of the active site cavity of RppA is larger than any other chalcone synthase-related enzymes found so far in plants and bacteria. RppA was also found to synthesize a C-methylated pyrone, 3,6-dimethyl-4-hydroxy-2-pyrone, by using acetoacetyl-CoA as the starter and methylmalonyl-CoA as an extender. Thus, the broad substrate specificity of RppA yields a wide variety of products.
    Zurück

  • Funa, N., Ohnishi, Y., Fujii, I., Shibuya, M., Ebizuka, Y., Horinouchi, S., 1999. A new pathway for polyketide synthesis in microorganisms. Nature 400, 897-899.
      
    Chalcone synthases, which biosynthesize chalcones (the starting materials for many flavonoids(1,2)), have been believed to be specific to plants. However, the rppA gene from the Gram-positive, soil-living filamentous bacterium Streptomyces griseus encodes a 372-amino-acid protein that shows significant similarity to chalcone synthases'. Several rppA-like genes are known, but their functions and catalytic properties have not been described. Here we show that a homodimer of RppA catalyses polyketide synthesis: it selects malonyl-coenzyme-A as the starter, carries out four successive extensions and releases the resulting pentaketide to cyclize to 1,3,6,8-tetrahydroxynaphthalene (THN). Site-directed mutagenesis revealed that, as in other chalcone synthases(4,5), a cysteine residue is essential for enzyme activity. Disruption of the chromosomal rppA gene in S. griseus abolished melanin production in hyphae, resulting in 'albino' mycelium. THN was readily oxidized to form 2,5,7-trihydroxy-1,4- naphthoquinone(flaviolin), which then randomly polymerized to form various coloured compounds. THN formed by RppA appears to be an intermediate in the biosynthetic pathways for not only melanins but also various secondary metabolites containing a naphthoquinone ring. Therefore, RppA is a chalcone-synthase- related synthase that synthesizes polyketides and is found in the Streptomyces and other bacteria.
    Zurück

  • Izumikawa, M., Shipley, P. R., Hopke, J. N., O'Hare, T., Xiang, L., Noel, J. P., Moore, B. S., 2003. Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2). Journal of Industrial Microbiology and Biotechnology 30, 510-515.
    Sequence analysis of the metabolically rich 8.7-Mbp genome of the model actinomycete Streptomyces coelicolor A3(2) revealed three genes encoding predicted type III polyketide synthases (PKSs). We report the inactivation, expression, and characterization of the type III PKS homologous SCO1206  gene product as 1,3,6,8-tetrahydroxynaphthalene synthase (THNS). Incubation of recombinant THNS with malonyl-CoA showed THN production, as demonstrated by UV and HPLC analyses. The K(m) value for malonyl-CoA and the k(cat) value for THN synthesis were determined spectrophotometrically to be 3.58+/-0.85 µM and 0.48+/-0.03 min(-1), respectively. The C-terminal region of S. coelicolor THNS, which is longer than most other bacterial and plant type III PKSs, was shortened by 25 amino acid residues and the resulting mutant was shown to be slightly more active (K(m)=1.97+/-0.19 µM, k(cat)=0.75+/-0.04 min(-1)) than the wild-type enzyme.
    Zurück

  • Li, S., Grüschow, S., Dordick, J. S., Sherman, D. H., 2007. Molecular analysis of the role of tyrosine 224 in the active site of Streptomyces coelicolor RppA, a bacterial type III polyketide synthase. Journal of Biological Chemistry 282, 12765-12772.
      
    Streptomyces coelicolor RppA (Sc-RppA), a bacterial type III polyketide synthase, utilizes malonyl-CoA as both starter and extender unit substrate to form 1,3,6,8-tetrahydroxynaphthalene (THN) (therefore RppA is also known as THN synthase (THNS)). The significance of the active site Tyr224 for substrate specificity has been established previously, and its aromatic ring is believed to be essential for RppA to select malonyl-CoA as starter unit. Herein, we describe a series of Tyr224 mutants of Sc-RppA including Y224F, Y224L, Y224C, Y224M, and Y224A that were able to catalyze a physiological assembly of THN, albeit with lower efficiency, challenging the necessity for the Tyr224 aromatic ring. Steady-state kinetics and radioactive substrate binding analysis of the mutant enzymes corroborated these unexpected results. Functional examination of the Tyr224 series of RppA mutants using diverse unnatural acyl-CoA substrates revealed the unique role of malonyl-CoA as starter unit substrate for RppA, leading to the development of a novel steric-electronic constraint model.
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