UC San Diego UC San Diego Electronic Theses and Dissertations Title Genome-Scale Reconstruction and Analysis of Eukaryotic Metabolic Networks Permalink https://escholarship.org/uc/item/5rq7d96x Author Hurlen, Natalie Christine Publication Date 2016-07-30 Supplemental Material https://escholarship.org/uc/item/5rq7d96x#supplemental Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO GENOME-SCALE RECONSTRUCTION AND ANALYSIS OF EUKARYOTIC METABOLIC NETWORKS A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Natalie Christine Hurlen Committee in charge: Professor Bernhard Ø. Palsson, Chair Professor Edward A. Dennis Professor Jeffrey D. Esko Professor Andrew D. McCulloch Professor Lanping Amy Sung 2006 Copyright Natalie Christine Hurlen, 2006 All rights reserved. The Dissertation of Natalie Christine Hurlen is approved, and it is acceptable in quality and form for publication on microfilm: Chair University of California, San Diego 2006 iii This Dissertation is dedicated to Mom, Pops, Mike, and “the boys” My dearest Erik and the Hurlen family and is in loving memory of Bohdan and Olga Chapla Henry and Eleanor Duarte iv We've called the human genome the book of life, but it's really three books: a history book, a shop manual and parts list, and a textbook of medicine more profoundly detailed than ever. Francis Collins, Director of the National Human Genome Research Institute v TABLE OF CONTENTS Signature Page .............................................................................................................iii Dedication.....................................................................................................................iv Epigraph........................................................................................................................v Table of Contents.........................................................................................................vi List of Figures ..............................................................................................................xi List of Tables..............................................................................................................xiv Preface…………………………………………………………………………........ xiv Acknowledgments......................................................................................................xvi Vita…………..............................................................................................................xix Abstract……………………………………………………………………………...xxi CHAPTER 1: INTRODUCTION ............................................................................... 1 1.1 What is systems biology? ......................................................................................... 1 1.2 Network reconstruction ............................................................................................ 1 1.3 Dissertation overview............................................................................................... 3 vi CHAPTER 2: TOOLS FOR GENOME-SCALE RECONSTRUCTION AND ANALYSIS.................................................................................................................... 6 2.1 Reconstruction resources.......................................................................................... 6 2.1.1 Genome annotation databases ................................................................... 6 2.1.2 Enzyme, reaction, and pathway databases ................................................ 7 2.1.3 Textbooks and review articles................................................................... 8 2.2 Constraint-based modeling....................................................................................... 8 2.2.1 Flux balance analysis................................................................................. 9 2.2.2 Phase planes and shadow price analysis.................................................. 10 2.2.3 In silico gene deletions ............................................................................ 11 CHAPTER 3: GENOME-SCALE RECONSTRUCTION OF THE SACCHAROMYCES CEREVISIAE METABOLIC NETWORK.......................... 15 3.1 Previous models of S. cerevisiae metabolism ........................................................ 15 3.2 Reconstruction of S. cerevisiae iND750 ................................................................ 17 3.2.1 Reconstruction procedure........................................................................ 17 3.2.2 Summary of S. cerevisiae iND750 .......................................................... 20 3.3 Validation of S. cerevisiae iND750 with a large-scale gene deletion study .......... 24 3.3.1 Comparison of in silico and in vitro growth phenotypes ........................ 24 vii 3.3.2 Analysis of false predictions by pathway and compartment................... 25 3.3.3 Analysis of false predictions by source................................................... 27 3.4 Conclusions ............................................................................................................ 36 CHAPTER 4: INTEGRATED ANALYSIS OF SACCHAROMYCES CEREVISIAE METABOLIC PHENOTYPES ........................................................ 50 4.1 In silico characterization of metabolic phenotypes ................................................ 50 4.1.1 S. cerevisiae phenotypic phase plane ...................................................... 51 4.1.2 Simulation of optimal metabolic phenotypes.......................................... 52 4.1.3 Further characterization of oxidative-fermentative phases ..................... 54 4.2 Integration of experimental data and in silico predictions ..................................... 56 4.3 Conclusions ............................................................................................................ 57 CHAPTER 5: GENOME-SCALE RECONSTRUCTION OF THE GLOBAL HUMAN METABOLIC NETWORK ...................................................................... 63 5.1 Previous models of mammalian metabolism.......................................................... 63 5.1.1 Small-scale, cell-specific metabolic models............................................ 64 5.1.2 Mammalian genome sequencing and the first genome-scale model ....... 65 5.1.3 Top-down reconstructions of human metabolism ................................... 66 5.2 Manual reconstruction of the global human metabolic network............................ 67 viii 5.2.1 Overall reconstruction strategy ............................................................... 67 5.2.2 Initial component list............................................................................... 68 5.2.3 Curation of network content.................................................................... 68 5.2.4 Functional validation and gap analysis ................................................... 72 5.2.5 The result, H. sapiens Recon 1................................................................ 72 5.3 Knowledge landscapes ........................................................................................... 74 5.4 Conclusions ............................................................................................................ 76 CHAPTER 6: GENE EXPRESSION ANALYSIS IN THE CONTEXT OF A GENOME-SCALE NETWORK............................................................................... 97 6.1 Integrated analysis of skeletal muscle metabolism ................................................ 97 6.1.1 The obesity epidemic............................................................................... 98 6.1.2 Metabolic gene expression in obese skeletal muscle .............................. 99 6.2 Tailoring the global metabolic network with pathway analysis........................... 103 6.3 Conclusions .......................................................................................................... 106 CHAPTER 7: CONCLUSIONS.............................................................................. 122 7.1 Contributions to the field...................................................................................... 123 7.1.1 Advancements in reconstructing eukaryotic metabolic networks......... 123 ix 7.1.2 Identification of metabolic knowledge gaps.......................................... 124 7.1.3 Integrated analysis of metabolic phenotypes......................................... 124 7.2 What’s next for S. cerevisiae iND750 and H. sapiens Recon 1? ......................... 125 7.3 Improving genome-scale reconstruction and analysis of eukaryotes................... 127 7.3.1 Enhancing component representations.................................................. 127 7.3.2 Improving communication with the research community..................... 130 7.3.3 Fine-tuning integration of gene-expression data................................... 130 7.4 Concluding remarks.............................................................................................. 132 BIBLIOGRAPHY..................................................................................................... 136 x LIST OF FIGURES Figure 1.1: The hierarchical relationship of network components.................................5 Figure 2.1: Overview of constraint-based modeling. ...................................................14 Figure 3.1: Overall reconstruction strategy for S. cerevisiae iND750. ........................38