The Identification of Genes and Enzymes in the Aldoxime-Nitrile Metabolising Pathway
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THE IDENTIFICATION OF GENES AND ENZYMES IN THE ALDOXIME-NITRILE METABOLISING PATHWAY Submitted to Waterford Institute of Technology for the Degree of Doctor of Philosophy By Tríona-Marie Dooley-Cullinane Pharmaceutical and Molecular Biotechnology Research Center (PMBRC) Waterford Institute of Technology, Waterford, Ireland Under the Supervision of Dr. Lee Coffey and Dr. Catherine O’Reilly 2019 DECLARATION The work described in this thesis isoriginal and was solely carried out by the author, and the work of others has been duly referenced in the text. No part of this thesis has been previously submitted for a degree at this or any other institute. Signed:_____________________ Date:_______________________ i ACKNOWLEDGEMENTS I owe a special thanks to my supervisors Dr. Lee Coffey and Dr. Catherine O’Reilly. I was fortunate to have been taught by both Lee and Catherine as an undergraduate student and their love of science and research was nothing short of inspiring. Thanks to both Catherine and Lee for your advice and support while I constructed this thesis, and for helping me find my way through the difficult days and months of writing. I would like to thank the technical staff of WIT, in particular Mari, Walter, Aidan, Pat and Stephen. In times of need, you were always on hand and I will forever be grateful for the guidance and advice. I am also indebted to my friends and fellow postgraduate students at WIT. Hazal thanks for always being a source of laughter and to Caio, your company in B19 made the long hours in the lab full of fun. I owe a special thanks to both Andrew and Caroline for the days of unwavering support, laughter and copious amounts of caffeine. They do say laughter is the best form of medicine. As the saying goes, your friends are the family you choose. If these past years have taught me anything, they have further instilled in me that I have chosen wisely. To both Sarah C and Sarah B, the endless days and nights of fun, dance parties and most importantly tea parties have gotten me through some of the hardest times. I will forever be grateful to you both. To my family, I cannot thank you enough for your patience, support and most importantly love. To my parents, you have both been amazing role models, showing that good work ethic and perseverance are the key to achieving and succeeding in life. Dad, I owe you a special thanks for showing me the importance of never giving up and for always giving advice and support. Mam, you have always believed in me and always been a source of encouragement and support, more than you realise. All I can hope is that one day, I become as well rounded and successful as you both, in all aspects of my life. Aoife, you helped to make the hardest days easier, I will be forever grateful for your company and sense of humor, you always knew when I needed it most. To my second family, the ii Gannon-Stephenson’s, you have made me feel like part of the furniture over the last nine years and have provided more support that you will ever know, I will be forever thankful. To Marcus, I don’t know where to begin. You have been on this journey with me since my undergraduate studies. You have witnessed all the ups and downs and your support and love has never waivered throughout. You have been there every day and night through it all and knew exactly what I needed, even when I didn’t. Your sense of humor and wit have made the longest days more bearable. I will forever be indebted to you for your years of guidance, support, patience and love. Finally, to Alice, this dissertation is dedicated to your memory. I hope that one day I can become half the woman you were, and I thank you for your encouragement and support during my younger years. iii ABSTRACT Biocatalysis is gaining much attention for the production of pharmaceutical intermediates, drug compounds and, fine chemicals. Biocatalysis, as a route of synthesis, boasts many benefits over traditional chemical synthesis. It can account for enantiopure compounds, lower waste production, decreases the need for potential purification and down-stream processing while also allowing the reactions to be carried out at milder conditions, such as lower temperatures and a relatively neutral pH (Gong et al. 2012, Singh et al. 2006). Due to the often low efficacy of racemic drugs or in fact the side effects caused by one of the enantiomers, enantiopure products are highly sought after (Albarrán-Velo et al. 2018). Thalidomide, a drug that was previously prescribed to treat morning sickness during pregnancy was sold as a safe and effective anti-emetic, in its racemic form. Unfortunately, years later the level of incidents of miscarriage and foetal birth defects observed amongst the women who were prescribed the drug led to the discovery that the S-enantiomer of the drug was teratogenic. Enzymes comprising the Aldoxime-Nitrile pathway are the focus of the body of work presented in this thesis. In 2010, it was reported that there were over 30 nitrile-containing pharmaceuticals on the market with another 20 at clinical trial stage (Fleming et al. 2010). Many nitrile containing drugs or intermediates may have been produced via chemical synthesis coupled with biocatalysis. Focusing on the identification of aldoxime dehydratase enzymes can offer a new, improved route to nitrile synthesis. The research presented in chapter two and published by (Dooley-Cullinane et al. 2016) presents a new high-throughput real-time (qPCR) for the detection of novel aldoxime dehydratase genes. The potential application of these genes/enzymes was reinforced by the Food and Drug Administration (FDA) approval of 11 nitrile containing pharmaceuticals since 2010. This is an indication as to what is to come with regard to an increase in market size for bio- pharmaceuticals produced by biocatalysis, in particular nitrile containing pharmaceuticals. The remaining enzymes which comprise the aldoxime-nitrile pathway, the nitrile- degrading enzymes such as nitrilases and nitrile hydratases (NHases), have been shown iv to display a broad substrate scope and complex nitrile substrates can be converted into their corresponding amides with the final enzyme, and amidase converting the amide to the corresponding carboxylic acids. The area of nitrile metabolism has been of great interest and will be into the foreseeable future (Huisman and Collier 2013, Gong et al. 2012). The body of work presented, details outputs and discoveries which form a part of the larger web of research undertaken by the molecular biocatalysis research group. The overall aim of research carried out by the group is the identification and discovery of novel genes and enzymes towards the production of industrially or biopharmaceutical relevant products. This thesis presents two novel molecular methods for the detection of genes within the aldoxime-nitrile pathway. A novel qPCR method was designed for the detection of aldoxime dehydratase genes. The second molecular method presented is a novel clade-specific touchdown conventional PCR which allows for the clade specific detection of novel nitrilase genes. Additionally, this protocol allows for the detection of nitrilase genes with predicted enzymatic activity in model substrates based on their clade classification. A novel nitrilase previously identified from Burkholderia sp. LC8 was cloned, expressed and characterised with results displaying a broad substrate range and excellent enantioselectivity towards mandelonitrile. The research also documents the discovery of a novel nitrilase partial sequence through the construction of a genomic fosmid library from genomic DNA of Rhodococcus erythropolis SET-1. This body of work involved the screening of fosmid clones for functional activity on 3-HGN. Further work presented a discussion on the attempts to elucidate the full nitrilase gene sequence via fosmid insert sequencing and also whole genome sequencing which led to the identification of a nitrile hydratase/amidase genomic cluster in R. erythropolis SET-1. v TABLE OF CONTENTS Acknowledgements ....................................................................................................... ii Abstract ........................................................................................................................ iv Table of Contents ......................................................................................................... vi Proposed Research…………………………………………………………………….1 1 Introduction ............................................................................................................... 5 1.1 Nitriles and their occurrence .............................................................................. 5 1.2 Toxicity of nitriles .............................................................................................. 5 1.3 Nitrile degrading pathways ................................................................................ 6 1.4 Nitrile hydrolysis ................................................................................................ 6 1.5 Nitrile metabolising enzymes ............................................................................. 7 1.5.1 Nitrilases (EC 3.5.5.1) ................................................................................. 7 1.5.2 Nitrilase classification and structure ........................................................... 9 1.5.3 Nitrilase activity ........................................................................................ 13 1.5.4 Nitrilase gene structure ............................................................................