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Rhodococcus Erythropolis and Gordonia Alkanivorans: Interesting Desulfurizing

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Rhodococcus Erythropolis and Gordonia Alkanivorans: Interesting Desulfurizing IN SILICO MODELING AND ANALYSIS FOR IMPROVING DESULFURIZING BACTERIAL STRAINS SHILPI AGGARWAL (M.Tech., Indian Institute of Technology, Roorkee, India) A THESIS SUBMITTED FOR THE DEGREE OF PHD OF ENGINEERING DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2012 Declaration DECLARATION I hereby declare that the thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. Shilpi Aggarwal 10 April 2013 i Acknowledgments ACKNOWLEDGMENTS I take this chance to express my sincere gratitude and love for my parents (Mr Subash and Mrs Renu) for their undying faith, encouragement, and unconditional love throughout my life. This PhD thesis is dedicated to them as I could have never come so far without their support. It is with immense pleasure and respect I take this opportunity to express my thankfulness to all those who have helped me in shaping my research career and making my stay in Singapore a truly memorable one. With the term ‘PhD’, the first person who comes to my mind is my supervisor, Prof I. A. Karimi. I take this chance to thank him for giving me an opportunity to pursue my research career under his able guidance. As a mentor he has made me acquire skills for critical and logical thinking. His directions and guidance has helped me get deeper insights into the subject and made my learning a great experience. Besides, the kindness and patience that he has shown in handling my mistakes during this research work has helped me become a better person. Truly, as I leave his group, I feel a little heavy for I will miss working smoothly under the guidance of such a wonderful supervisor. It was indeed a privilege to have worked with him. I extend my sincere thanks to Dr. D. Y. Lee for his timely inputs for my research work. His ideas and suggestions have always made me achieve better results and enhanced my knowledge of the subject. I would also like to thank Prof Kilbane from Illinois Institute of Technology, Illinois, Chicago for sharing his knowledge and experience with working on biodesulfurization. His novel ideas and deeper insights about the subject have added new dimensions to my work. ii Acknowledgments I would also like to thank Prof Y. P. Ting and Dr. Rudiyanto Gunawan for their kind acceptance to be on the panel of examiners during the qualifying exam. I also thank Prof. Li Zhi and Dr.Yan Kun Lin for being my thesis examiners and spending time on evaluating this thesis. I wish to admire and thank all the unknown reviewers of our publications, who gave constructive feedbacks on all our manuscripts and helped us to bring the best out of this research. I also extend my thanks to my friend, Rajib Saha from Penn State University, Pennsylvania for his regular guidance and discussions about genome scale modeling. His timely support with the subject has greatly helped in enhancing my knowledge and completion of this work. There are no words to thank my dear friends Nidhi, Susheela, Naresh, Manoj, Himani, Mona, Dr. Mukta, Shobha, Tanvi, Vaani, Sadegh, Rahul, and all others, who have helped me sail through this journey with their kind words and encouragement at all times. Special thanks to my labmates (Hanifah, Kunna,Vasanth, Kefeng, Anoop, Rajnish, Karthik, Nishu) and friends at NUS (Sumit, Shivom, Srinath, Vaibhav, Krishna, and more), who made my stay in Singapore and at NUS all the more comfortable and enjoyable. And most importantly, I thank my elder sister Surabhi, my brother Shivam, my nephew Devom, and my niece Ananya for their love and affection throughout my life. I am always grateful to my grandparents as nothing would have been possible without their blessings. Finally, I thank my cousins and the entire family for always being my source of inspiration. Their love, continued support, and motivation have always been helpful. iii Table of contents TABLE OF CONTENTS DECLARATION _________________________________________________________ i ACKNOWLEDGMENTS __________________________________________________ ii TABLE OF CONTENTS __________________________________________________ iv SUMMARY ___________________________________________________________ x NOMENCLATURE_____________________________________________________ xiv ABBREVIATIONS _____________________________________________________ xv LIST OF FIGURES ____________________________________________________ xvii LIST OF TABLES ______________________________________________________ xix 1 Introduction _____________________________________________________ 1 1.1 Need for desulfurizarion _____________________________________________ 2 1.2 Hydrodesulfurization _______________________________________________ 2 1.3 Biodesulfurization __________________________________________________ 3 1.4 Rhodococcus erythropolis and Gordonia alkanivorans: interesting desulfurizing bacterial strains __________________________________________________________ 5 1.5 In silico modeling ___________________________________________________ 8 1.6 Research objectives _________________________________________________ 9 1.7 Thesis outline ____________________________________________________ 11 2 Literature review ________________________________________________ 13 2.1 Biological desulfurization of fossil fuels ________________________________ 13 iv Table of contents 2.1.1 Need for fossil fuels desulfurization _________________________________________ 13 2.1.2 Hydrodesulfurization _____________________________________________________ 15 2.1.3 Biodesulfurization _______________________________________________________ 16 2.1.3.1 Types of sulfur compounds ___________________________________________ 17 2.1.3.2 Biotechnology for desulfurization ______________________________________ 18 2.1.3.3 Mechanisms of biodesulfurization _____________________________________ 20 2.1.3.3.1 Kodama pathway (destructive): _____________________________________ 20 2.1.3.3.2 4S pathway (non-destructive) ______________________________________ 21 2.1.3.3.3 Other mechanisms: _______________________________________________ 22 2.1.3.4 Biodesulfurization studies with rhodococci strains ________________________ 24 2.1.3.5 Biodesulfurization studies with gordoniae strains _________________________ 35 2.1.4 Need for in silico holistic studies of desulfurizing strains ________________________ 40 2.2 Systems biology for in silico metabolic modeling ________________________ 42 2.3 In silico mathematical models _______________________________________ 44 2.3.1 Kinetic models: _________________________________________________________ 44 2.3.2 Stoichiometric models: ___________________________________________________ 46 2.4 Research focus ___________________________________________________ 48 3 Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis ______________________________________________ 51 3.1 Introduction _____________________________________________________ 51 3.2 Materials and methods _____________________________________________ 53 3.2.1 Model construction ______________________________________________________ 53 3.2.2 Experimental data sources for model validation _______________________________ 55 3.3 Results and discussion _____________________________________________ 55 3.3.1 Model for sulfur metabolism in R. erythropolis ________________________________ 55 3.3.2 Model validation ________________________________________________________ 56 v Table of contents 3.3.3 Analysis of sulfur metabolism using alternate sources __________________________ 58 3.3.3.1 In silico growth on alternate sulfur sources ______________________________ 58 3.3.3.2 Effect of sulfate on desulfurizing activity ________________________________ 60 3.3.4 Effect of carbon source ___________________________________________________ 61 3.4 Summary ________________________________________________________ 63 4 Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies ___________________________________ 65 4.1 Introduction ______________________________________________________ 65 4.2 Materials and methods _____________________________________________ 67 4.2.1 Reconstruction of genome-scale model ______________________________________ 67 4.2.2 Experimental data _______________________________________________________ 69 4.2.3 Flux balance analysis _____________________________________________________ 71 4.2.4 Reaction and gene essentiality analysis ______________________________________ 72 4.3 Results and discussion______________________________________________ 72 4.3.1 Reconstructed genome-scale model ________________________________________ 72 4.3.2 Model validation ________________________________________________________ 74 4.3.3 Essential genes and reactions ______________________________________________ 77 4.3.4 Minimal medium ________________________________________________________ 79 4.3.5 Desulfurization in the presence of cysteine and methionine _____________________ 80 4.3.6 Effects of medium components on desulfurization activity and growth of R. erythropolis 83 4.3.6.1 Relative effectiveness of carbon sources ________________________________ 83 4.3.6.2 Combined effect of carbon and nitrogen sources _________________________ 84 4.3.7 Comparison with E. coli model _____________________________________________ 87 4.4 Summary ________________________________________________________
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