Analysis of vitamin B6 biosynthesis in Arabidopsis thaliana
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1 Research Collection Doctoral Thesis Analysis of vitamin B6 biosynthesis in Arabidopsis thaliana Author(s): Tambasco Studart, Marina Publication Date: 2007 Permanent Link: Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library
2 DISS. ETH NO ANALYSIS OF VITAMIN B6 BIOSYNTHESIS IN ARABIDOPSIS THALIANA A dissertation submitted to ETH ZURICH for the degree of DOCTOR OF SCIENCES presented by MARINA TAMBASCO STUDART M.Sc. Genetics and Evolution, Federal University of São Carlos born 21 May 1975 citizen of Brazil accepted on the recommendation of Prof. Dr. Nikolaus Amrhein, examiner Prof. Dr. Hauke Hennecke, co-examiner Dr. Teresa B. Fitzpatrick, co-examiner 2007
3 Summary i SUMMARY Vitamin B6 is an essential metabolite that can act as a cofactor in a broad range of biochemical reactions and has recently also been shown to act as a potent antioxidant. Microorganisms and plants biosynthesize the vitamin de novo, whereas animals must obtain it from dietary sources. Classical biochemical and genetic studies on the vitamin B6 biosynthesis pathway have been mainly restricted to Escherichia coli, where it is derived from 1-deoxyxylulose 5-phosphate (DXP) and 4-phosphohydroxy-L-threonine (4-PHT) by the action of the PdxA and PdxJ proteins. However, at the outset of this thesis, it was becoming clear from studies in fungi that a different pathway is probably in operation in most organisms with the main exception certain members of the γ division of the proteobacteria, which includes E. coli. Organisms which have this alternative pathway do not have a copy of PdxJ but instead are characterized by the presence of two genes, PDX1 and PDX2, the products of which have been predicted to function together as a glutamine amidotransferase. Vitamin B6 biosynthesis had not been studied in plants, with the exception of one preliminary report in Therefore, the aim of this study was to investigate biochemical and physiological aspects of the biosynthesis of this vitamin in the model plant Arabidopsis thaliana, by using a combination of in vivo and in vitro approaches. In contrast to what has been tacitly stated in the literature, during this study the biosynthesis of vitamin B6 in plants was found to occur independently of the isoprenoid pathway intermediate DXP. Moreover, we could identify three PDX1 homologs (named PDX1.1, PDX1.2 and PDX1.3) and a single PDX2 homolog in the Arabidopsis genome. The localization of the PDX proteins was experimentally shown to be cytosolic, contradicting a single preliminary report in which vitamin B6 was claimed to be synthesized in chloroplasts. Spatial and temporal expression analyses reveal that the PDX genes are expressed in most of the tissues and throughout the life cycle. On the other hand, a completely discrepant expression pattern was observed for PDX1.2. Indeed, only two of the PDX1 genes, PDX1.1 and PDX1.3, were found to be functional in vitamin B6 biosynthesis, shown by in vivo and in vitro analyses. Examination of pdx1.1 and pdx1.3 knockout mutants revealed retardation of root growth, which is much more pronounced in pdx1.3, indicating that this homolog is more important for normal growth of the plant. The phenotype of pdx1.3 was indeed associated with a lower vitamin B6 content when compared to pdx1.1. Knocking out both PDX1.1 and PDX1.3 is lethal for the plant resulting in growth arrest at the globular stage of embryo development, corroborating the result that PDX1.2 is not functional in vitamin B6 biosynthesis. The function of this homolog remains to be established.
4 ii Summary Analysis of pdx2 knockout lines shows that this single copy gene is also essential for plant viability in that its disruption results in an arrest of embryo development at the same stage as that observed for the double pdx1.1/pdx1.3 mutant. The functionality of PDX2 in vitamin B6 biosynthesis was proven by the ability to rescue the pdx2 phenotype exclusively by vitamin B6 supplementation. This was corroborated by complementation experiments in Saccharomyces cerevisiae. Moreover, vitamin B6 reconstitution could be accomplished in vitro in the presence of PDX2, glutamine, either of the two functional PDX1 proteins and the substrates ribose 5-phosphate or ribulose 5-phosphate and glyceraldehyde 3-phosphate or dihydroxyacetone phosphate. In addition, glutamine hydrolysis by PDX2 could be separately demonstrated and was shown to be enhanced by a functional PDX1, confirming the protein pair as a glutamine amidotransferase. The PDX1/PDX2 protein complex is now referred to as PLP synthase, since the cofactor form of the vitamin, pyridoxal 5 -phosphate (PLP), was shown to be the reaction product. A model of the Arabidopsis PLP synthase is provided based on the three dimensional structure of the Bacillus subtilis counterpart, which was solved towards the completion of this thesis. This model indicates remote glutaminase and synthase active sites separated by a putative tunnel for delivery of ammonia from the former to the active site of the latter. Comparison of the rates of PLP formation and glutamine hydrolysis demonstrates coordination between the two active sites of the PLP synthase complex, possibly mediated by a residue at the base of the predicted ammonia tunnel.
5 Zusammenfassung iii ZUSAMMENFASSUNG Vitamin B6 ist ein essentielles Stoffwechselprodukt, das in einer Vielzahl biochemischer Reaktionen als Kofaktor wirkt und kürzlich auch als wirksames Antioxidans nachgewiesen wurde. Mikroorganismen und Pflanzen synthetisieren das Vitamin de novo, während Tiere es mit der Nahrung aufnehmen müssen. Klassische biochemische und genetische Untersuchungen zum Biosyntheseweg von Vitamin B6 haben sich auf Escherichia coli beschränkt, in dem das Vitamin aus Deoxyxylulose 5-phosphat (DXP) und 4-Phosphohydroxy-L-Threonin (4-PHT) durch die Proteine PdxA und PdxJ gebildet wird. Zu Beginn dieser Promotionsarbeit liessen jedoch an Pilzen durchgeführte Arbeiten erkennen, dass in den meisten Organismen, mit der hauptsächlichen Ausnahme von einigen Mitgliedern der Gruppe der γ-proteobakterien, darunter E. coli, ein anderer Weg vorkommt. Organismen, die diesen alternativen Syntheseweg benutzen, enthalten an Stelle des PdxJ Gens die Gene PDX1 und PDX2, deren Produkte gemeinsam als Glutaminamidotransferase fungieren sollen. Mit Ausnahme eines vorläufigen Berichts aus dem Jahre 1992, war die Biosynthese von Vitamin B6 noch nicht in Pflanzen untersucht worden. Es war daher das Ziel dieser Arbeit, biochemische und physiologische Aspekte der Biosynthese dieses Vitamins in der Modellpflanze Arabidopsis thaliana mit Hilfe einer Kombination von in vivo und in vitro Ansätzen zu untersuchen. Im Gegensatz zu stillschweigenden Annahmen in der Literatur, zeigte sich im Laufe dieser Arbeit, dass die Biosynthese von Vitamin B6 in Pflanzen unabhängig vom Intermediat des Isoprenoidbiosynthesewegs, DXP, verläuft. Weiterhin konnten wir drei PDX1 homologe Gene (PDX1.1, PDX1.2, PDX1.3) und ein einziges PDX2 homologes Gen im Arabidopsis Genom indentifizieren. Wie experimentell gezeigt werden konnte, sind die PDX Proteine cytosolisch, im Widerspruch zu einem früheren einzelnen Bericht, demzufolge Vitamin B6 in Chloroplasten synthetisiert werden soll. Analysen der zeitlichen und räumlichen Expression zeigen, dass die PDX Gene in den meisten Geweben, und während der ganzen Lebensspanne der Pflanze exprimiert werden. Ein völlig abweichendes Expressionsmuster wurde für PDX1.2 beobachtet. Tatsächlich sind nur zwei der PDX1 Gene, d.h. PDX1.1 und PDX1.3, in der Biosynthese von Vitamin B6 funktionell, wie in vivo und in vitro Analysen übereinstimmend bewiesen. Die Untersuchung der pdx1.1 und pdx1.3 Knockoutmutanten ergab eine Reduktion des Wurzelwachstums, die in pdx1.3 wesentlich stärker ausgeprägt war. Dies weist daraufhin, dass dieses Homologe eine grössere Bedeutung für das normale Wachstum der Pflanze hat. Im Vergleich zu pdx1.1, hatte die pdx1.3 Mutante einen geringeren Gehalt an Vitamin B6. Der gleichzeitige Knockout von PDX1.1 und PDX1.3 ist letal, indem das Wachstum im globulären Stadium der Embryoentwicklung blockiert ist.
6 iv Zusammenfassung Hierdurch wird das Ergebnis bestätigt, dass PDX1.2 in der Vitamin B6 Biosynthese nicht aktiv ist. Die Funktion dieses Homologen muss noch ermittelt werden. Die Analyse von PDX2 Knockoutlinien ergab, dass dieses in nur einer Kopie vorliegende Gen für die Pflanzen überlebenswichtig ist, da seine Zerstörung zur Einstellung des Embryowachstums im gleichen Stadium erfolgt, wie es für die Doppelmutante pdx1.1/pdx1.3 der Fall war. Die Funktionalität von PDX2 in der Biosynthese von Vitamin B6 wurde nachgewiesen, indem der pdx2 Phänotyp durch die Zugabe von Vitamin B6 aufgehoben werden konnte. Dieser Befund wurde durch das Ergebnis von Komplentationsversuchen in Saccharomyces cerevisiae unterstützt. Weiterhin wurde Vitamin B6 in vitro in Gegenwart von PDX2, Glutamin, einem der beiden funktionellen PDX1 Proteine und den Substraten Ribose 5-Phosphat oder Ribulose 5-Phosphat und Glycerinaldehyd 3- Phosphat oder Dihydroxyacetonphosphat synthetisiert. Zusätzlich konnte die Hydrolyse von Glutamin durch PDX2 getrennt nachgewiesen werden. Die Aktivierung der Hydrolyse durch ein funktionelles PDX1 bestätigt das Paar der beiden Proteine als Glutaminamidotransferase. Der PDX1/PDX2 Proteinkomplex wird nunmehr als PLP Synthase bezeichnet, weil die Kofaktorform des Vitamins, Pyridoxal 5 -Phosphat (PLP) als Reaktionsprodukt nachgewiesen wurde. Ein Modell der Arabidopsis PLP Synthase wird vorgestellt, das auf der dreidimensionalen Struktur des entsprechenden Bacillus subtilis Komplexes beruht, die gegen Abschluss der vorliegenden Doktorarbeit gelöst wurde. Dieses Modell weist auf voneinander entfernt liegende aktive Zentren für die Glutaminase- und Synthaseaktivitäten hin, die vermutlich durch einen Tunnel miteinander verbunden sind, durch den Ammoniak vom ersteren zum letzteren angeliefert wird. Ein Vergleich der Raten der Bildung von PLP und der Hydrolyse von Glutamin weist auf eine Koordination der beiden aktiven Zentren des PLP Synthase Komplexes hin, die möglicherweise durch einen Aminosäurerest an der Basis des mutmasslichen Ammoniaktunnels bewerkstelligt wird. iv
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