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Synthetic Biology underpins advances in the bioeconomy

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology. 

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

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  • JOURNAL ARTICLE
    Kelwick RJR, Ricci L, Chee SM, Bell D, Webb A, Freemont Pet al., 2019,

    Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics

    , Synthetic Biology, Vol: 3, ISSN: 2397-7000

    The polyhydroxyalkanoates (PHAs) are microbially-produced biopolymers that could potentially be used as sustainable alternatives to oil-derived plastics. However, PHAs are currently more expensive to produce than oil-derived plastics. Therefore, more efficient production processes would be desirable. Cell-free metabolic engineering strategies have already been used to optimise several biosynthetic pathways and we envisioned that cell-free strategies could be used for optimising PHAs biosynthetic pathways. To this end, we developed several Escherichia coli cell-free systems for in vitro prototyping PHAs biosynthetic operons, and also for screening relevant metabolite recycling enzymes. Furthermore, we customised our cell-free reactions through the addition of whey permeate, an industrial waste that has been previously used to optimise in vivo PHAs production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by ∼50%. In cell-free transcription-translation prototyping reactions, GC-MS quantification of cell-free 3-hydroxybutyrate (3HB) production revealed differences between the activities of the Native ΔPhaC_C319A (1.18 ±0.39 µM), C104 ΔPhaC_C319A (4.62 ±1.31 µM) and C101 ΔPhaC_C319A (2.65 ±1.27 µM) phaCAB operons that were tested. Interestingly, the most active operon, C104 produced higher levels of PHAs (or PHAs monomers) than the Native phaCAB operon in both in vitro and in vivo assays. Coupled cell-free biotransformation/transcription-translation reactions produced greater yields of 3HB (32.87 ±6.58 µM) and these reactions were also used to characterise a Clostridium propionicum Acetyl-CoA recycling enzyme. Together, these data demonstrate that cell-free approaches complement in vivo workflows for identifying additional strategies for optimising PHAs production.

  • JOURNAL ARTICLE
    Poulton J, Wolde PRT, Ouldridge TE, 2019,

    Non-equilibrium correlations in minimal dynamical models of polymer copying

    , Proceedings of the National Academy of Sciences, Vol: 116, Pages: 1946-1951, ISSN: 0027-8424

    Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these non-equilibrium states are created, and analyze the accuracy and efficiency of a family of dynamical models that produce persistent copies. For the weakest chemical driving, when polymer growth occurs in equilibrium, both the copy accuracy and, more surprisingly, the efficiency vanish. At higher driving strengths, accuracy and efficiency both increase, with efficiency showing one or more peaks at moderate driving. Correlations generated within the copy sequence, as well as between template and copy, store additional free energy in the copied polymer and limit the single-site accuracy for a given chemical work input. Our results provide insight in the design of natural self-replicating systems and can aid the design of synthetic replicators.

  • JOURNAL ARTICLE
    Kylilis N, Riangrungroj P, Lai H-E, Salema V, Angel Fernandez L, Stan G-BV, Freemont PS, Polizzi KMet al., 2019,

    Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications

    , ACS SENSORS, Vol: 4, Pages: 370-378, ISSN: 2379-3694
  • JOURNAL ARTICLE
    Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2019,

    The exit time finite state projection scheme: bounding exit distributions and occupation measures of continuous-time Markov chains

    We introduce the exit time finite state projection (ETFSP) scheme, atruncation-based method that yields approximations to the exit distribution andoccupation measure associated with the time of exit from a domain (i.e., thetime of first passage to the complement of the domain) of time-homogeneouscontinuous-time Markov chains. We prove that: (i) the computed approximationsbound the measures from below; (ii) the total variation distances between theapproximations and the measures decrease monotonically as states are added tothe truncation; and (iii) the scheme converges, in the sense that, as thetruncation tends to the entire state space, the total variation distances tendto zero. Furthermore, we give a computable bound on the total variationdistance between the exit distribution and its approximation, and we delineatethe cases in which the bound is sharp. We also revisit the related finite stateprojection scheme and give a comprehensive account of its theoreticalproperties. We demonstrate the use of the ETFSP scheme by applying it to twobiological examples: the computation of the first passage time associated withthe expression of a gene, and the fixation times of competing species subjectto demographic noise.

  • BOOK CHAPTER
    Ouldridge TE, Brittain RA, Wolde PRT, 2018,

    The power of being explicit: demystifying work, heat, and free energy in the physics of computation

    Interest in the thermodynamics of computation has revived in recent years,driven by developments in science, economics and technology. Given theconsequences of the growing demand for computational power, the idea ofreducing the energy cost of computations has gained new importance.Simultaneously, many biological networks are now interpreted asinformation-processing or computational systems constrained by their underlyingthermodynamics. Indeed, some suggest that low-cost, high-density biologicalsystems may help to mitigate the rising demand for computational power and the"end" of Moore's law of exponential growth in the density of transistors. In this chapter we address widespread misconceptions about thermodynamics andthe thermodynamics of computation. In particular, we will argue against thegeneral perception that a measurement or copy operation can be performed at nocost, against the emphasis placed on the significance of erasure operations,and against the careless discussion of heat and work. While not universal,these misconceptions are sufficiently prevalent (particularly withininterdisciplinary contexts) to warrant a detailed discussion. In the process,we will argue that explicitly representing fundamental processes is a usefultool, serving to demystify key concepts. We first give a brief overview of thermodynamics, then the history of thethermodynamics of computation - particularly in terms of copy and measurementoperations inherent to classic thought experiments. Subsequently, we analysethese ideas via an explicit biochemical representation of the entire cycle ofSzilard's engine. In doing so we show that molecular computation is both apromising engineering paradigm, and a valuable tool in providing fundamentalunderstanding.

  • JOURNAL ARTICLE
    Kyrou K, Hammond AM, Galizi R, Kranjc N, Burt A, Beaghton AK, Nolan T, Crisanti Aet al., 2018,

    A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes

    , NATURE BIOTECHNOLOGY, Vol: 36, Pages: 1062-+, ISSN: 1087-0156
  • JOURNAL ARTICLE
    Kelly CL, Harris AWK, Steel H, Hancock EJ, Heap JT, Papachristodoulou Aet al., 2018,

    Synthetic negative feedback circuits using engineered small RNAs

    , NUCLEIC ACIDS RESEARCH, Vol: 46, Pages: 9875-9889, ISSN: 0305-1048
  • JOURNAL ARTICLE
    Trantidou T, Dekker L, Polizzi K, Ces O, Elani Yet al., 2018,

    Functionalizing cell-mimetic giant vesicles with encapsulated bacterial biosensors

    , INTERFACE FOCUS, Vol: 8, ISSN: 2042-8898
  • JOURNAL ARTICLE
    Waters AJ, Capriotti P, Gaboriau DCA, Papathanos PA, Windbichler Net al., 2018,

    Rationally-engineered reproductive barriers using CRISPR & CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster

    , SCIENTIFIC REPORTS, Vol: 8, ISSN: 2045-2322
  • JOURNAL ARTICLE
    Yunus IS, Wichmann J, Woerdenweber R, Lauersen KJ, Kruse O, Jones PRet al., 2018,

    Synthetic metabolic pathways for photobiological conversion of CO2 into hydrocarbon fuel

    , METABOLIC ENGINEERING, Vol: 49, Pages: 201-211, ISSN: 1096-7176
  • JOURNAL ARTICLE
    Schaerli Y, Jimenez A, Duarte JM, Mihajlovic L, Renggli J, Isalan M, Sharpe J, Wagner Aet al., 2018,

    Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

    , MOLECULAR SYSTEMS BIOLOGY, Vol: 14, ISSN: 1744-4292
  • JOURNAL ARTICLE
    Yunus IS, Jones PR, 2018,

    Photosynthesis-dependent biosynthesis of medium chain-length fatty acids and alcohols

    , METABOLIC ENGINEERING, Vol: 49, Pages: 59-68, ISSN: 1096-7176
  • JOURNAL ARTICLE
    Oling D, Lawenius L, Shaw W, Clark S, Kettleborough R, Ellis T, Larsson N, Wigglesworth Met al., 2018,

    Large Scale Synthetic Site Saturation GPCR Libraries Reveal Novel Mutations That Alter Glucose Signaling

    , ACS SYNTHETIC BIOLOGY, Vol: 7, Pages: 2317-2321, ISSN: 2161-5063
  • JOURNAL ARTICLE
    Aw R, McKay PF, Shattock RJ, Polizzi KMet al., 2018,

    A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization.

    , Protein Expr Purif, Vol: 149, Pages: 43-50

    Pichia pastoris (Komagataella phaffi) has been used for recombinant protein production for over 30 years with over 5000 proteins reported to date. However, yields of antibody are generally low. We have evaluated the effect of secretion signal peptides on the production of a broadly neutralizing antibody (VRC01) to increase yield. Eleven different signal peptides, including the murine IgG1 signal peptide, were combinatorially evaluated for their effect on antibody titer. Strains using different combinations of signal peptides were identified that secreted approximately 2-7 fold higher levels of VRC01 than the previous best secretor, with the highest yield of 6.50 mg L-1 in shake flask expression. Interestingly it was determined that the highest yields were achieved when the murine IgG1 signal peptide was fused to the light chain, with several different signal peptides leading to high yield when fused to the heavy chain. Finally, we have evaluated the effect of using a 2A signal peptide to create a bicistronic vector in the attempt to reduce burden and increase transformation efficiency, but found it to give reduced yields compared to using two independent vectors.

  • JOURNAL ARTICLE
    Rajakumar PD, Gowers G-OF, Suckling L, Foster A, Ellis T, Kitney RI, McClymont DW, Freemont PSet al., 2018,

    Rapid Prototyping Platform for Saccharomyces cerevisiae Using Computer-Aided Genetic Design Enabled by Parallel Software and Workcell Platform Development.

    , SLAS Technol

    Biofoundries have enabled the ability to automate the construction of genetic constructs using computer-aided design. In this study, we have developed the methodology required to abstract and automate the construction of yeast-compatible designs. We demonstrate the use of our in-house software tool, AMOS, to coordinate with design software, JMP, and robotic liquid handling platforms to successfully manage the construction of a library of 88 yeast expression plasmids. In this proof-of-principle study, we used three fluorescent genes as proxy for three enzyme coding sequences. Our platform has been designed to quickly iterate around a design cycle of four protein coding sequences per plasmid, with larger numbers possible with multiplexed genome integrations in Saccharomyces cerevisiae. This work highlights how developing scalable new biotechnology applications requires a close integration between software development, liquid handling robotics, and protocol development.

  • JOURNAL ARTICLE
    Ceroni F, Ellis T, 2018,

    The challenges facing synthetic biology in eukaryotes

    , NATURE REVIEWS MOLECULAR CELL BIOLOGY, Vol: 19, Pages: 481-482, ISSN: 1471-0072
  • JOURNAL ARTICLE
    Kylilis N, Tuza ZA, Stan G-B, Polizzi KMet al., 2018,

    Tools for engineering coordinated system behaviour in synthetic microbial consortia

    , NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723
  • JOURNAL ARTICLE
    Liu D, Mannan AA, Han Y, Oyarzun DA, Zhang Fet al., 2018,

    Dynamic metabolic control: towards precision engineering of metabolism

    , JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, Vol: 45, Pages: 535-543, ISSN: 1367-5435
  • JOURNAL ARTICLE
    Beal J, Haddock-Angelli T, Baldwin G, Gershater M, Dwijayanti A, Storch M, de Mora K, Lizarazo M, Rettberg Ret al., 2018,

    Quantification of bacterial fluorescence using independent calibrants

    , PLOS ONE, Vol: 13, ISSN: 1932-6203
  • JOURNAL ARTICLE
    Bena CE, Grob A, Isalan M, Bosia C, Ceroni Fet al., 2018,

    Commentary: synthetic addiction extends the productive life time of engineered Escherichia coli populations

    , FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, Vol: 6, ISSN: 2296-4185

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