Algorithms for Improving the Predictive Power of Flux Balance Analysis Dissertation zur Erlangung des Grades Doktor der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Heinrich-Heine Universitaet Duesseldorf von Abdelmoneim Mahmoud Amer Desouki M.Sc., Computer Science geboren am 09. 10. 1975 in Beheira, Egypt Heinrich-Heine University 2016 Referent: Prof. Dr. Martin Lecher Korreferent: Prof. Dr. Oliver Ebenhöh Tag der mündlichen Prüfung 16.Juni.2016 ii To my Parents, my wife, Mariam , Omar and Ahmed. iii Contents DEDICATION ...................................................................................................................... ii LIST OF TABLES .............................................................................................................. vii LIST OF FIGURES ........................................................................................................... viii ABBREVIATIONS .............................................................................................................. ix ACKNOWLEDGMENTS ..................................................................................................... x ABSTRACT ......................................................................................................................... xi ZUSAMMENFASSUNG ................................................................................................... xiii PUBLICATIONS................................................................................................................. xv Chapter 1: Introduction ........................................................................................................... 1 1.1 Metabolism ................................................................................................................ 1 1.2 Metabolic Models ...................................................................................................... 2 1.3 Flux Balance Analysis(FBA) ..................................................................................... 3 1.4 Elementary Flux Modes (EFM) ................................................................................. 5 1.5 Problems in FBA ....................................................................................................... 5 1.6 Sybil .......................................................................................................................... 6 1.6.1 Reading metabolic models ...................................................................................... 8 1.6.2 Running FBA .......................................................................................................... 9 1.6.3 Running FVA ........................................................................................................ 10 1.6.4 Running MTF ....................................................................................................... 10 1.7 Organization of the thesis ....................................................................................... 13 Chapter 2 Loopless Flux ..................................................................................................... 14 2.1 Introduction ............................................................................................................ 14 2.2 Characterization of internal cycles .......................................................................... 14 2.3 Removing internal cycles from a given flux distribution (CycleFreeFlux) .............. 16 2.4 Speed ....................................................................................................................... 18 2.5 Cycle-free sampling ................................................................................................. 19 2.6 Cycle-free flux variability analysis .......................................................................... 20 2.7 Enumeration of internal cycles................................................................................. 23 Chapter 3 ccFBA: building MetabOlic Models with ENzyme kineTics (MOMENT) from FBA models in R .................................................................................................................. 25 3.1 Introduction ............................................................................................................. 25 3.2 Algorithm and Implementation ................................................................................ 25 3.2 Results ..................................................................................................................... 27 iv 3.2.1 Escherichia coli ..................................................................................................... 27 3.2.2 Saccharomyces cerevisiae ..................................................................................... 32 Chapter 4 sybilEFBA: An R package for expression-based FBA ........................................ 34 4.1 Introduction ............................................................................................................. 34 4.1.1 Existing Expression based methods ...................................................................... 34 4.1.2 Overview of chapter 4 ........................................................................................... 35 4.2 FECorr Algorithm .................................................................................................... 36 4.2.1 Run FVA:.............................................................................................................. 39 4.2.2 Fit a piecewise linear function: ............................................................................. 39 4.2.3 Find closest flux distribution: ................................................................................ 40 4.2.4 Mapping gene expression to reactions................................................................... 41 4.2.5 Applying FECorr .................................................................................................. 41 4.3 Function ATMFBA ................................................................................................. 46 4.3.1 Scaling expression levels by kcat ........................................................................... 46 4.3.2 Optimization of activity thresholds ....................................................................... 47 4.3.3 Results .................................................................................................................. 50 4.4 eFBA-gene ............................................................................................................... 51 Application to the Holm dataset..................................................................................... 55 Chapter 5 Discussion, Conclusion and future work ............................................................. 57 5.1 loopless FBA ........................................................................................................... 57 5.1.1 Alternative methods to calculate thermodynamically feasible solutions ............... 57 5.1.2 Runtime comparisons ............................................................................................ 57 5.1.3 Biases introduced by CycleFreeFlux ..................................................................... 58 5.1.4 Conclusion ............................................................................................................ 58 5.1.5 Future work ........................................................................................................... 58 5.2 Cost-constrained FBA .............................................................................................. 59 5.2.1 A general framework to incorporate solvent capacity constraints into FBA.......... 59 5.2.2 Comparison of ccFBA to other algorithms that include solvent capacity constraints ....................................................................................................................................... 60 5.2.3 Shortcomings of ccFBA and related approaches ................................................... 60 5.2.4 Future work ........................................................................................................... 60 5.3 Expression-based FBA ............................................................................................ 62 5.3.1 FECorr: deriving quantitative flux-expression level estimates from data across experiments .................................................................................................................... 62 v 5.3.2 ATM-FBA: automatic thresholding for reaction and protein activities ................. 62 5.3.3 eFBA-gene: reconciling gene rather than reaction activities with expression data 63 5.3.4 Alternative strategies to utilize expression data in FBA predictions ..................... 63 5.3.5 Future work ........................................................................................................... 64 Appendix A ........................................................................................................................... 67 References............................................................................................................................. 70 vi LIST OF TABLES Table Page TABLE 1 RUNTIME COMPARISON BETWEEN LL-FBA (SCHELLENBERGER ET AL., 2011) AND CYCLEFREEFBA. ... 19 TABLE 2. EXPERIMENTALLY MEASURED AND MOMENT-PREDICTED MAXIMUM GROWTH RATES (IN MMOL/GDW/H) FOR E. COLI ON