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Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus Capsulatus

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Downloaded from orbit.dtu.dk on: Oct 09, 2021 Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus Lieven, Christian Publication date: 2018 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Lieven, C. (2018). Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus. Technical University of Denmark. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus PhD Thesis by Christian Lieven February 2018 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus PhD thesis written by Christian Lieven Title collage by Maja Rennig based on illustrations by Christian Lieven Main Supervisor: Nikolaus Sonnenschein © PhD Thesis 2018 Christian Lieven Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kemitorvet, Building 220 2800 Kgs. Lyngby Denmark II III Preface This thesis is written as a partial fulfillment of the requirements to obtain a PhD degree at the Technical University of Denmark. The work presented in this thesis was carried out between March 2015 and February 2018 at the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark, Kgs. Lyngby, and was supervised by Senior Scientist Nikolaus Sonnenschein. The Innovation Fund Denmark and the Novo Nordisk Foundation provided funding. ______________________ Christian Lieven Kgs. Lyngby, February 2018 IV Abstract Climate-change induced food scarcity is a grim prospect for the future of humanity. Alas, increasingly detrimental effects of global warming and overpopulation are predicted to beget this outlook by the year 2050. Fortunately, the production of single-cell protein (SCP) from microbial fermentations presents an answer since it circumvents having to expand a spatially limited agriculture. It represents a controllable, scalable approach to food production that can be developed on a number of industrial waste products. The greenhouse gas methane is released abundantly into the atmosphere by both agricultural and industrial processes. To capitalize on this resource, the establishment of the protein-rich obligate methanotroph Methylcococcus capsulatus as an SCP product has been pursued. In addition, other methanotrophic organisms have been considered as cell factories for the production of chemicals from methane. In this thesis, we recount the interplay between methane and the environment and outline the process of a genome-scale metabolic model (GEM) reconstruction. We then illuminate methods from software development that could streamline and quality control the reconstruction process, after which we continue to introduce existing genome-scale metabolic models of methanotrophs and their applications in biotechnology. The main merit of this work lies in presenting memote (metabolic model tests), a set of community-curated test cases and the corresponding software, which enable the automated quality control of GEMs independent from reconstruction platforms or analyses software. Memote strongly supports publicly hosted and version controlled models, which we hope facilitates cross-community collaboration and research transparency. Furthermore, we present the first manually curated GEM of Methylococcus capsulatus. The model comprises 750 genes, 877 metabolites and 898 reactions and V has been used to investigate the mode of electron transfer in this organism. Since it combines multi-layered biochemical and genomic information into one single knowledgebase, the availability of a GEM for M. capsulatus is an invaluable prerequisite for rational strain engineering towards an improved SCP production. VI Dansk Resumé Fødevareknaphed induceret af klimaændringer giver menneskehedens fremtid dårlige udsigter, og tiltagende skadelige følgevirkninger af global opvarmning og overbefolkning forudsiges at indtræde frem mod 2050. Heldigvis udgør produktion af enkeltcelleprotein (SCP) fra mikrobielle fermenteringer en mulig løsning, da det omgår udfordringen med et rumligt begrænset landbrug. Det repræsenterer en kontrollerbar, skalerbar tilgang til fødevareproduktion, der kan baseres på en række industriaffaldsprodukter. Drivhusgassen metan frigives i atmosfæren ved både landbrug og industrielle processer. For at udnytte denne ressource er det forsøgt at etablere den proteinrige obligatoriske methanotroph Methylcococcus capsulatus som et SCP- produkt. Derudover er andre metanotrofe organismer blevet betragtet som cellefabrikker til fremstilling af kemikalier fra metan. I denne afhandling gennemgås samspillet mellem metan og miljøet og konstruktionen af en genomskala metabolisk model (GEM) skitseres. Vi belyser derefter metoder fra softwareudvikling, der kan lette og kontrollere genopbygningsprocessen, hvorefter vi fortsætter med at introducere eksisterende metaboliske modeller for metanotrofer og deres anvendelser inden for bioteknologi. Hovedværdien af dette arbejde ligger i at udviklingen af memote (metabolic model tests), et sæt af community-udviklede testcases og den tilsvarende software. Memote understøtter og opfordrer offentligt hostede og versionsstyrede modeller, som vi håber letter samarbejde mellem grupper og gennemsigtigheden af forskningen. Desuden præsenterer vi den første manuelt kuraterede GEM af Methylococcus capsulatus. Modellen indeholder 750 gener, 877 metabolitter og 898 reaktioner og er blevet brugt til at undersøge elektrontransporten i denne organisme. Da en VII GEM for M. capsulatus kombinerer biokemisk og genomisk information i en enkelt viden database, er tilgængeligheden af en sådan model en uvurderlig forudsætning for SCP-produktion. VIII Acknowledgements In the short three years that I’ve spent as a PhD student, I’ve met a number of wonderful people here at the Center for Biosustainability, many of whom I’ve not only shared memorable experiences with but to whom I also owe a great deal of gratitude. Before I begin, however, I ought to remark that none of this would have been possible if Birgitta Ebert had not made me aware of the job offer for this project in the first place. Thank you, Birgitta for being the initial impetus to these three truly exciting years! Now, first of all I’d like to thank my main supervisor Nikolaus Sonnenschein not only for ultimately giving me the opportunity to pursue a PhD at the Center for Biosustainability, but also for enduring the many, probably very confusing, meetings on the complexities of metabolism in M. capsulatus. Your patience, trust, feedback and support has inspired me, and your approachable, jovial but sharp way motivated me to perpetually improve upon my own work. I thank you for giving me the opportunity to attend several international research conferences, exposing me to a great network of renowned experts. Next, for granting me a chair at the table of the SIMS group, I’d like to thank Markus Herrgård. I greatly benefited from your drive and your vast experience and knowledge during these past three years. Being able to look to you for guidance has helped me immensely, particularly in my first year and on many occasions thereafter. I appreciate that you’ve taken the time to hear out my ideas, giving me new perspectives through feedback and critique. I thank Leander Petersen, Sten Bay Jorgensen, Budi Juliman Hidayat, Subir Kumar Nandi, John Villadsen, Eleni Ntokou and Krist Gernaey for the countless hours of discussions about their experiences with M. capsulatus, their excitement about new results and their competent feedback. My thanks go out to the DD-DeCaF team, Svetlana Kutuzova, Henning Redestig, Ali Kaafarni, Matyas Fodor and, most importantly, Mortiz E. Beber, for letting me observe and learn their software engineering skills, through following the same spring plans, collaborating on memote, and helping at the software carpentry course together. IX For allowing me to visit his group on very short notice, I’d like to thank Jens Nielsen at Chalmers. I’ve had a great time and truly some of the most insightful discussions in my time as a PhD student. Parizad Babaei, Benjamín Sánchez Barja, Eduard Kerkhoven and Dimitra Lappa have been able to shed light on important user requirements for the development of memote, so by extension I’d like to express my gratitude to them too. The warm welcome I received when I started at the SIMS group three years ago was tremendously relieving, for this, the excellent atmosphere ever since, and their support along the way, I’d like to thank Miguel Campodonico, Sumesh Sukumara, Emre Özdemir, Marta Matos, Ida Bonde, Kristian Jensen, Anne Sofie Lærke Hansen,
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