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Dissecting the Indigo Pathway

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Dissecting the Indigo Pathway Dissecting the indigo pathway By Tim Daykin B. App. Sci (Hons) Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy June 2011 Department of Biotechnology and Environmental Biology RMIT University i Declaration I certify that except where due acknowledgement has been made, the work is that of the author alone; the work has not been submitted previously, in whole or in part, to qualify for any other academic award; the content of the thesis is the result of work which has been carried out since the official commencement date of the approved research program; any editorial work paid or unpaid, carried out by a third party is acknowledged; and, ethics procedures and guidelines have been followed. Tim Daykin Date: ii Acknowledgements I would like to sincerely thank my supervisor Associate Professor Trevor Stevenson for his help and guidance throughout my candidature, especially in the last six months. I appreciate his candour, the thorough scrutiny of my data and his ongoing advice, all of which was critical to me submitting my thesis. Big thanks also go to Professor David Stalker for the chance to ‘look after his baby’. This project was inspired by Dave and I appreciate the opportunity he gave me and the knowledge I gained from his know-how. Special gratitude also goes to Trevor and Dave for the constant light relief they provided from the stress of life in the lab and the perspective I gained from their experiences. I would like to acknowledge Associate Professor Peter Smooker and Dr Manvendra Saxena for providing me with the Red disruption system that was crucial to my research. To Dr Greg Nugent, Dr Veera Chikkala and Kim Stevenson I appreciate the ear you provided when I needed someone to bounce ideas off. To all of my fellow scientists and students who called the plant biotech lab home over the year’s thanks for all the support you afforded. Recognition also must to go to Natalie Kikidopoulos, Aya Taki, Shannon Fernandes and Dr Fiona Baird for putting up with my antics. Furthermore, thanks to Shannon for all the technical help she provided. In addition, thanks must go to Dr Lisa Dias and Dr Kylie White for helping me with formatting. To the inhabitants of the ‘Swamp’: Teigs, Liam, Adam, Whit and my brother Sadie, thanks for the good times. I needed them and you guys provided them, it kept me sane. Finally to my family, especially my parents David and Eileen, the biggest thanks go to them, for their ongoing support and encouragement. iii Thesis Abstract Indigo is a vibrant blue pigment synthesised by plants and bacteria. This study examined the mechanisms by which plants generate indole, an intermediate common to both the indigo and tryptophan biosynthetic pathways. Cleavage of Indole-3-glycerol phosphate (I3GP) by the tryptophan synthase (TS) αβ enzyme complex forms indole for subsequent tryptophan biosynthesis. Specifically, indole synthesis is catalysed by the TS α sub-unit, encoded by the trp A gene, leading to this sub-unit being described as an ‘indole synthase’. Typically, TS α sub-units only catalyse indole synthesis when bound to a specific TS β sub-unit counterpart. However, there does exist in plants enzymes capable of catalysing indole synthesis independently. In Zea mays , there is an indole synthase (IS) enzyme ten times more efficient than the TS αβ enzyme complex at catalysing indole biosynthesis from I3GP. When the maize indole synthase gene was expressed in a TS α deficient E. coli strain it complemented the trp A mutation, indicating that the enzyme encoded by this gene produced indole as an intermediate in tryptophan biosynthesis in the absence of a plant specific TS β sub-unit. The removal of tryptophanase activity by targeted mutagenesis in a host E. coli strain eliminated the alternative route for tryptophan biosynthesis from indole. Complementation by the Z. mays IS of the trp A mutation suggests that the IS forms a functional enzyme complex with an E. coli TS β sub-unit. A Polygonum tinctorium cDNA library was screened via hybridisation with the Z. mays IS gene and by functional analysis. The unsuccessful hybridisation suggested the absence of a gene homologous to the maize IS gene within P. tinctorium , whilst failure of the cDNA library to rescue the E. coli trp A mutant strain indicated the non-existance of a functional clone. iv Table of Contents Declaration.................................................................................................................................ii Acknowledgements...................................................................................................................iii Thesis Abstract.........................................................................................................................iv Table of Contents ......................................................................................................................v Abbreviations ............................................................................................................................x List of Figures..........................................................................................................................xii List of Tables ...........................................................................................................................xv 1 Chapter One: Review of literature .................................................................................1 1.1 History of indigo dyeing .................................................................................................1 1.1.1 Cultural significance of indigo........................................................................2 1.1.2 Advances in dyeing practices ..........................................................................2 1.1.3 The era of synthetic indigo..............................................................................3 1.1.3.1 Indigo white.......................................................................................................5 1.2 Natural indigo production..............................................................................................7 1.2.1 Indigo producing plants...................................................................................7 1.2.1.1 Isatis tinctoria....................................................................................................8 1.2.1.2 Polygonum tinctorium ....................................................................................10 1.2.2 Indigo synthesis in plants ..............................................................................12 1.2.2.1 Indican and isatin B........................................................................................13 1.2.3 Indole conversion ...........................................................................................17 1.2.3.1 Hydroxylase mediated indole conversion.......................................................17 1.2.4 Microbial biosynthesis of indigo...................................................................19 1.2.4.1 Naphthalene dioxygenase ...............................................................................19 1.2.4.2 Bacterial CYP’s ...............................................................................................21 1.2.4.3 Indole oxygenase.............................................................................................22 1.3 Tryptophan Biosynthesis..............................................................................................24 1.3.1 The tryptophan pathway...............................................................................24 1.3.2 Tryptophan synthase .....................................................................................28 1.3.3 Enzyme mutants within the tryptophan biosynthetic pathway.................30 1.3.4 Sub-unit association.......................................................................................32 1.4 The indigo-tryptophan paradigm................................................................................34 1.4.1 Indole synthase...............................................................................................34 v 1.4.2 Tryptophanase................................................................................................38 1.4.3 Rationale .........................................................................................................38 1.5 Aims of the present study .............................................................................................42 2 Chapter Two: General materials and methods..........................................................44 2.1 General procedures.......................................................................................................44 2.2 Media and antibiotics....................................................................................................44 2.2.1 Antibiotic stock solutions...............................................................................44 2.2.2 LB agar............................................................................................................45 2.2.3 LB broth..........................................................................................................45 2.2.4 M9 minimal media (+ CAA) agar.................................................................45 2.2.5 M9 minimal media (+ CAA) broth...............................................................45 2.3 Bacterial strains and plasmids.....................................................................................46
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