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Bioprospecting for Microorganisms and Enzymes with Biorefining Potential

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Bioprospecting for Microorganisms and Enzymes with Biorefining Potential Bioprospecting for Microorganisms and Enzymes with Biorefining Potential by Laura Frances Lyons Supervisors Dr Kerrie Farrar and Dr Justin Pachebat A thesis submitted at the Institute of Biological, Environmental and Rural Sciences (Aberystwyth University), for the degree of Doctor of Philosophy. 2015 1 2 Declaration This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Signed ...................................................................... (candidate) Date ........................................................................ STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where *correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signed ..................................................................... (candidate) Date ........................................................................ [*this refers to the extent to which the text has been corrected by others] STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signed ..................................................................... (candidate) Date ........................................................................ Word count of thesis: 53 812 3 4 Acknowledgments Well here’s the cheesey part (mmm cheese, sorry, let us continue…). Firstly, I would like to thank my supervisors Kerrie and Justin, especially for giving me a kick up the arse when I needed it. Also, it can’t be easy reading draft after draft of long winded explanations of relatively simple things. Massive thanks must go out to Sarah Hawkins, who has always been there in times of trouble (like the hot water baths…) as well as when things were actually going smoothly (I’m sure that must have happened once…). Personally, I think every lab should have a Sarah! Also, thank you to Naomi (along with Sarah) for her patience in training me in the first year. I would like to thank everyone in the labs I have worked in, except Abhi as he stole everything; didn’t make up buffers when he’d used them up, and generally left a mess everywhere (just kidding). Everyone in the student offices over the past four years obviously deserves thanks. Especially Magda, who brought me back down to earth when everything was going wrong, and Alice for her distractions of field work, as well as maintaining a working atmosphere in the office. Not forgetting Dave and Tim for the endless football discusions and Fantasy Football rivalry. Naheed and Colin must also be acknowledged for their great knowledge of proteins and patience when teaching me. Thank you to David Bryant and Naheed for also reading through chapters and making me think outside of the box. Also, thanks to Joe, Ana, Richard and Eli for not talking about work on Friday evenings down The Glen. And Jenny, Tim, Dave and Alina for all the fun times! Plus, Mark, Jan, Pip and Liz for the rugby times! And of course Spicer with her lunchtime walks with MollyDog! I must also acknowledge Manny (Romain Jugal), for his hard work and dedication in the six months he worked with me as part of his MSc. The lab was not the same after Christmas songs in March! (Où est la piscine?!) I’d like to also extend thanks to people outside of academia who have encouraged and congratulated me over the extent of my PhD, including Andy, Nige, Olive, Iris, Kellie, Marc and many more. The Sunday quiz in Scholars was always a good end to the week, thank you Tom. Of course, I thank my family for their endless support, especially my mom and dad for the gift of rent for Christmas and my birthday! And my brother, who occasionally knows when he is wrong, but has always encouraged his little sister. Mostly, I would like to thank Grace for putting up with me, supporting me and generally just trying to make life a bit simpler and easier. Finally I would like to thank my funders because without them I would not have had this amazing experience and potentially helped the human race (yes, I can still change the world even after doing a PhD!). Also, thank you for reading this! I hope it’s not too tedious and I apologise, I’m sure most of the pages are pictures! 5 6 Summary The rise of biorefining and application of biotechnology to combat climate change and accomplish energy security is a necessity. There have already been steps to produce sustainable biofuels and products throughout the world. However, not all processes are economically viable due to costs of enzymes, pre-treatments, and scale-ups. In this project Miscanthus sp. was the main source of bacterial isolation due to its bioenergy characteristics as a low-input high-output crop. Specifically, due to the high sugar content of harvested senesced Miscanthus. The aim of this project was to discover novel microbes and enzymes with potential to contribute to the generation of fuels and chemicals from plant biomass. Specifically, we aimed to isolate and characterise enzymes capable of efficiently releasing sugars from pre-treated lignocellulosic biomass, for subsequent fermentation to ethanol and platform chemicals. Aerobic bacteria were cultured from harvested chipped Miscanthus and soil surrounding Miscanthus crops and were characterised morphologically, functionally and taxonomically. Bacteria in our collection included amongst others: Pseudomonas sp., Burkholderia sp., Variovorax paradoxus, Luteibacter sp. and Bacillus sp.. The collection was screened for carbon utilisation using cellulose (in the form of carboxymethyl cellulose), xylan (from beechwood) and starch by enzymatic activity, at a range of temperatures and pHs. From the bacterial library, 88.5% of cultures showed cellulase activity, 93.2% xylanase activity, 79.7% starch degradation activity over the temperature or pH range, with 66.2% demonstrating activity over all three assays. Proteins were isolated from bacteria that demonstrate effective starch utilisation for further characterisation. Bacterial isolates that exhibited xylan utilisation at high pH and temperature were characterised by whole genome sequencing to identify interesting enzymes and pathways using bioinformatics software CLC genomics and Seed RAST. Finally, homologous proteins have been modelled using Phyre2 and 3DLigandSite to analyse structure and binding sites. This work was part of the wider BEACON project which aimed to establish Wales as a Biorefining Centre of Excellence. BEACON built integrated ‘Green Supply Chains’ with a focus on developing new routes to functional, cost competitive products using biomass rather than fossil fuels. 7 8 Contents Declaration .................................................................................................................... 3 Acknowledgments ........................................................................................................ 5 Summary ....................................................................................................................... 7 List of Abbreviations ................................................................................................... 13 List of Figures .............................................................................................................. 17 List of Tables ............................................................................................................... 20 Chapter 1 Introduction ................................................................................................................ 23 1.1 The problem: Climate change ............................................................................... 23 1.2 A solution: Biorefining .......................................................................................... 23 1.2.1 Miscanthus as a biorefining feedstock ....................................................................... 28 1.3 Hydrolysis of the plant cell wall ............................................................................ 29 1.3.1 Lignocellulolytic enzymes; application in a biorefining context ................................ 33 1.3.2 Cellulose and cellulases .............................................................................................. 34 1.3.3 Hemicellulose and hemicellulases ............................................................................. 39 1.3.4 Starch and amylases ................................................................................................... 41 1.3.5 Pre-treatment of biomass .......................................................................................... 44 1.4 Microbial sources of lignocellulolytic enzymes .................................................... 47 1.4.1 Glycosyl Hydrolases .................................................................................................... 52 1.5 Metabolic Engineering and Synthetic Biology ...................................................... 53 1.5.1 Metabolic Engineering ............................................................................................... 53 1.5.2 Synthetic Biology ........................................................................................................ 55 1.6 Commercial development of biorefining .............................................................
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