Turing patterns are common but not robust

Turing patterns (TPs) underlie many fundamental developmental processes, but they operate over narrow parameter ranges, raising the conundrum of how evolution can ever discover them. Here we explore TP design space to address this question and to distill design rules. We exhaustively analyze 2- and 3-node biological candidate Turing systems: crucially, network structure alone neither determines nor guarantees emergent TPs. A surprisingly large fraction (>60%) of network design space can produce TPs, but these are sensitive to even subtle changes in parameters, network structure and regulatory mechanisms. This implies that TP networks are more common than previously thought, and evolution might regularly encounter prototypic solutions. Importantly, we deduce compositional rules for TP systems that are almost necessary and sufficient (96% of TP networks contain them, and 95% of networks implementing them produce TPs). This comprehensive network atlas provides the blueprints for identifying natural TPs, and for engineering synthetic systems.

[1]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[2]  J. Stark,et al.  Network motifs: structure does not determine function , 2006, BMC Genomics.

[3]  Paul D. W. Kirk,et al.  Cellular population dynamics control the robustness of the stem cell niche , 2015, Biology Open.

[4]  Heather A. Harrington,et al.  Nuclear to cytoplasmic shuttling of ERK promotes differentiation of muscle stem/progenitor cells , 2014, Development.

[5]  W. Lim,et al.  Defining Network Topologies that Can Achieve Biochemical Adaptation , 2009, Cell.

[6]  M. Stumpf,et al.  Systems biology (un)certainties , 2015, Science.

[7]  James Sharpe,et al.  Key Features of Turing Systems are Determined Purely by Network Topology , 2017, Physical Review X.

[8]  Christian R. Boehm,et al.  Programmed hierarchical patterning of bacterial populations , 2017, Nature Communications.

[9]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[10]  Neil Dalchau,et al.  Beyond activator-inhibitor networks: the generalised Turing mechanism , 2018, 1803.07886.

[11]  Ping Liu,et al.  Bifurcation analysis of reaction–diffusion Schnakenberg model , 2013, Journal of Mathematical Chemistry.

[12]  Shigeru Kondo,et al.  Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation , 2010, Science.

[13]  T. Hwa,et al.  Growth Rate-Dependent Global Effects on Gene Expression in Bacteria , 2009, Cell.

[14]  Paul Kirk,et al.  Conditional random matrix ensembles and the stability of dynamical systems , 2015, 1505.02920.

[15]  L Wolpert,et al.  Local inhibitory action of BMPs and their relationships with activators in feather formation: implications for periodic patterning. , 1998, Developmental biology.

[16]  A. R. Palmer Symmetry Breaking and the Evolution of Development , 2004, Science.

[17]  James Sharpe,et al.  High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals , 2016, eLife.

[18]  James Sharpe,et al.  A unified design space of synthetic stripe-forming networks , 2014, Nature Communications.

[19]  Xia Sheng,et al.  Bayesian design of synthetic biological systems , 2011, Proceedings of the National Academy of Sciences.

[20]  David Iron,et al.  Stability analysis of Turing patterns generated by the Schnakenberg model , 2004, Journal of mathematical biology.

[21]  H. Meinhardt,et al.  Pattern formation by local self-activation and lateral inhibition. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[22]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[23]  J E Ferrell,et al.  The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. , 1998, Science.

[24]  Heather A. Harrington,et al.  Cellular compartments cause multistability and allow cells to process more information. , 2013, Biophysical journal.

[25]  J. Ferrell,et al.  Modeling the Cell Cycle: Why Do Certain Circuits Oscillate? , 2011, Cell.

[26]  Shigeru Kondo,et al.  Interactions between zebrafish pigment cells responsible for the generation of Turing patterns , 2009, Proceedings of the National Academy of Sciences.

[27]  Qi Ouyang,et al.  Identifying network topologies that can generate turing pattern. , 2016, Journal of theoretical biology.

[28]  Jeremy Gunawardena,et al.  Information Integration and Energy Expenditure in Gene Regulation , 2016, Cell.

[29]  J Raspopovic,et al.  Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients , 2014, Science.

[30]  A. M. Arias,et al.  Transition states and cell fate decisions in epigenetic landscapes , 2016, Nature Reviews Genetics.

[31]  Andrew W. Murray,et al.  The Ups and Downs of Modeling the Cell Cycle , 2004, Current Biology.

[32]  Jamie A Davies,et al.  2- and 3-dimensional synthetic large-scale de novo patterning by mammalian cells through phase separation , 2016, Scientific Reports.

[33]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[34]  H. Meinhardt,et al.  A theory of biological pattern formation , 1972, Kybernetik.

[35]  J. Timmer,et al.  Supporting Online Material Material and Methods , 2022 .

[36]  Zhe Tan,et al.  Polyamide membranes with nanoscale Turing structures for water purification , 2018, Science.

[37]  Paul T. Sharpe,et al.  Periodic stripe formation by a Turing-mechanism operating at growth zones in the mammalian palate , 2012, Nature Genetics.

[38]  Luis Diambra,et al.  Genetically Encoded Sender–Receiver System in 3D Mammalian Cell Culture , 2013, ACS synthetic biology.

[39]  Ruth E Baker,et al.  Turing's model for biological pattern formation and the robustness problem , 2012, Interface Focus.

[40]  Jeff Hasty,et al.  Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules , 2016, PloS one.

[41]  Luis Diambra,et al.  Cooperativity To Increase Turing Pattern Space for Synthetic Biology , 2014, ACS synthetic biology.

[42]  U. Alon,et al.  Negative autoregulation speeds the response times of transcription networks. , 2002, Journal of molecular biology.

[43]  L. Wolpert Positional information and the spatial pattern of cellular differentiation. , 1969, Journal of theoretical biology.

[44]  Pamela A. Silver,et al.  Making Cellular Memories , 2010, Cell.

[45]  Ricard V Solé,et al.  Toward Synthetic Spatial Patterns in Engineered Cell Populations with Chemotaxis. , 2016, ACS synthetic biology.

[46]  Mark Isalan,et al.  A three-step framework for programming pattern formation. , 2017, Current opinion in chemical biology.

[47]  Jonathon Howard,et al.  Turing's next steps: the mechanochemical basis of morphogenesis , 2011, Nature Reviews Molecular Cell Biology.

[48]  Michael P H Stumpf,et al.  Topological sensitivity analysis for systems biology , 2014, Proceedings of the National Academy of Sciences.

[49]  J. Sharpe,et al.  Positional information and reaction-diffusion: two big ideas in developmental biology combine , 2015, Development.

[50]  James Sharpe,et al.  An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients , 2010, Molecular systems biology.

[51]  Sungrim Seirin-Lee,et al.  The bifurcation analysis of turing pattern formation induced by delay and diffusion in the Schnakenberg system , 2016 .

[52]  Hans Meinhardt,et al.  The Algorithmic Beauty of Sea Shells , 2003, The Virtual Laboratory.