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Algorithms for Improving the Predictive Power of Flux Balance Analysis

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Algorithms for Improving the Predictive Power of Flux Balance Analysis 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
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