Exploring mechanisms of xylem cell wall patterning with dynamic models

Abstract

Contents 1 General introduction 1.1 Xylem cell wall patterning 1.2 Pattern formation mechanisms 1.2.1 Reaction-diffusion mechanisms 1.2.2 Not every pattern is a Turing pattern 1.3 Small GTPases 1.3.1 Small GTPases in reaction-diffusion systems 1.3.2 Mass conservation 1.4 Microtubules 1.4.1 Microtubule properties 1.4.2 Microtubules and cell wall structure 1.4.3 Microtubule self-organisation 1.5 ROPs and microtubules in xylem patterning 1.6 Aim and thesis outline 3.7.3 Effect of alternative anisotropic diffusion scenarios 3.7.4 Diffusion tensor rotation 3.7.5 Preferred spiral angles 3.7.6 Diffusion term decomposition 3.7.7 Parameters of models with ROP-dependent ROP diffusion 4 The role of nucleation complexes in cortical microtubule array homogeneity and patterning 4.1 Introduction 4.2 Results 4.2.1 A simplified model of transversely oriented microtubules reproduces the inhomogeneity problem 4.2.2 Tubulin diffusion is too fast for sufficient local variation in microtubule growth velocities 4.2.3 Nucleation complexes are preferentially inserted at microtubules 4.2.4 Local limitation of nucleation complexes can solve the inhomogeneity problem 4.3 Discussion 4.4 Methods 4.4.1 Simulation setup 4.4.2 Core microtubule dynamics 4.4.3 Protoxylem band and gap regions 4.4.4 Basic nucleation modes 4.4.5 Tubulin dynamics 4.4.6 Nucleation complexes 4.4.7 Model parameters 4.4.8 Measures of heterogeneity 4.4.9 Experimental measurements 4.5 Supplementary figures 4.6 Supplementary tables 4.7 Appendices 4.7.1 Steady state densities for non-interacting microtubules 4.7.2 Calculating maximal total microtubule length and initial growth speed 4.7.3 Estimation of nucleation complex parameters 5 Protoxylem microtubule patterning requires ROP pattern co-alignment, realistic microtubule-based nucleation, and sufficient microtubule flexibility 5.1 Introduction 5.2 Results 5.2.1 Model outline 5.2.2 Strong co-alignment of the microtubule array with a pre-existing band pattern facilitates rapid microtubule band formation 5.2.3 Microtubule flexibility can lead to density loss from bands 5.2.4 Locally saturating nucleation helps to keep bands populated with semiflexible microtubules, even for misaligned starting arrays viii CONTENTS 5.2.5 Array patterning must be robust against large variations in observed microtubule dynamics 5.2.6 Band-gap separation factors outside the measured parameter differences 5.3 Discussion 5.4 Methods 5.4.1 Simulation setup 5.4.2 Nucleation modes 5.4.3 Expected mismatch angles 5.4.4 Semiflexible microtubules 5.4.5 Cell data simulations 5.4.6 Summary statistics 5.5 Supplementary figures 5.6 Appendices 5.6.1 Parameters for locally saturating nucleation 5.6.2 Persistence length calculations 6 General discussion 6.1 Insights into mechanisms of xylem patterning 6.1.1 A ROP-based Turing pattern as the basis of xylem patterning 6.1.2 Protoxylem ROP pattern orientation 6.1.3 Coexistence in ROP and microtubule patterns 6.1.4 ROP-microtubule interplay 6.2 Insights into non-xylem membrane patterning 6.2.1 Coexistence in non-xyle...