Pathways to cellular supremacy in biocomputing

Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found.A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU grant number 820699). T.E.G. was supported by a Royal Society University Research Fellowship (grant UF160357) and BrisSynBio, a BBSRC/ EPSRC Synthetic Biology Research Centre (grant BB/L01386X/1). P.Z. was supported by the EPSRC Portabolomics project (grant EP/N031962/1). P.C. was supported by SynBioChem, a BBSRC/EPSRC Centre for Synthetic Biology of Fine and Specialty Chemicals (grant BB/M017702/1) and the ShikiFactory100 project of the European Union’s Horizon 2020 research and innovation programme under grant agreement 814408

iii TREE AND SOIL NITROGEN RESPONSES TO ALTERNATIVE GROUND COVER MANAGEMENT STRATEGIES IN ORGANIC APPLE PRODUCTION

ii ACKNOWLEDGMENTS I would like to thank my committee members for their excellent guidance and support in this process. I would also like to thank the BioAg Program of the Center for Sustainin

Tuning Promoter Strengths for Improved Synthesis and Function of Electron Conduits in <i>Escherichia coli</i>

Introduction of the electron transfer complex MtrCAB from <i>Shewanella oneidensis</i> MR-1 into a heterologous host provides a modular and molecularly defined route for electrons to be transferred to an extracellular inorganic solid. However, an <i>Escherichia coli</i> strain expressing this pathway displayed limited control of MtrCAB expression and impaired cell growth. To overcome these limitations and to improve heterologous extracellular electron transfer, we used an <i>E. coli</i> host with a more tunable induction system and a panel of constitutive promoters to generate a library of strains that separately transcribe the <i>mtr</i> and cytochrome <i>c</i> maturation (<i>ccm</i>) operons over 3 orders of magnitude. From this library, we identified strains that show 2.2 times higher levels of MtrC and MtrA and that have improved cell growth. We find that a ∼300-fold decrease in the efficiency of MtrC and MtrA synthesis with increasing <i>mtr</i> promoter activity critically limits the maximum expression level of MtrC and MtrA. We also tested the extracellular electron transfer capabilities of a subset of the strains using a three-electrode microbial electrochemical system. Interestingly, the strain with improved cell growth and fewer morphological changes generated the largest maximal current per cfu, rather than the strain with more MtrC and MtrA. This strain also showed ∼30-fold greater maximal current per cfu than its <i>ccm</i>-only control strain. Thus, the conditions for optimal MtrCAB expression and anode reduction are distinct, and minimal perturbations to cell morphology are correlated with improved extracellular electron transfer in <i>E. coli</i>