Imperial College London

Tom Ellis

Faculty of EngineeringDepartment of Bioengineering

Professor of Synthetic Genome Engineering
 
 
 
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Contact

 

+44 (0)20 7594 7615t.ellis Website CV

 
 
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Location

 

704Bessemer BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

74 results found

Walker K, Goosens V, Das A, Graham A, Ellis Tet al., 2019, Engineered cell-to-cell signalling within growing bacterial cellulose pellicles, Microbial Biotechnology, Vol: 12, Pages: 611-619, ISSN: 1751-7915

Bacterial cellulose is a strong and flexible biomaterial produced at high yields by Acetobacter species and has applications in health care, biotechnology and electronics. Naturally, bacterial cellulose grows as a large unstructured polymer network around the bacteria that produce it, and tools to enable these bacteria to respond to different locations are required to grow more complex structured materials. Here, we introduce engineered cell‐to‐cell communication into a bacterial cellulose‐producing strain of Komagataeibacter rhaeticus to enable different cells to detect their proximity within growing material and trigger differential gene expression in response. Using synthetic biology tools, we engineer Sender and Receiver strains of K. rhaeticus to produce and respond to the diffusible signalling molecule, acyl‐homoserine lactone. We demonstrate that communication can occur both within and between growing pellicles and use this in a boundary detection experiment, where spliced and joined pellicles sense and reveal their original boundary. This work sets the basis for synthetic cell‐to‐cell communication within bacterial cellulose and is an important step forward for pattern formation within engineered living materials.

Journal article

Det-Udom R, Gilbert C, Liu L, Prakitchaiwattana C, Ellis T, Ledesma Amaro Ret al., 2019, Towards semi-synthetic microbial communities: Enhancing soy sauce fermentation properties in B. subtilis co-cultures, Microbial Cell Factories, Vol: 18, ISSN: 1475-2859

BackgroundMany fermented foods and beverages are produced through the action of complex microbial communities. Synthetic biology approaches offer the ability to genetically engineer these communities to improve the properties of these fermented foods. Soy sauce is a fermented condiment with a vast global market. Engineering members of the microbial communities responsible for soy sauce fermentation may therefore lead to the development of improved products. One important property is the colour of soy sauce, with recent evidence pointing to a consumer preference for more lightly-coloured soy sauce products for particular dishes.ResultsHere we show that a bacterial member of the natural soy sauce fermentation microbial community, Bacillus, can be engineered to reduce the ‘browning’ reaction during soy sauce production. We show that two approaches result in ‘de-browning’: engineered consumption of xylose, an important precursor in the browning reaction, and engineered degradation of melanoidins, the major brown pigments in soy sauce. Lastly, we show that these two strategies work synergistically using co-cultures to result in enhanced de-browning.ConclusionsOur results demonstrate the potential of using synthetic biology and metabolic engineering methods for fine-tuning the process of soy sauce fermentation and indeed for many other natural food and beverage fermentations for improved products.

Journal article

Rajakumar PD, Gower G, Suckling L, Kitney R, McClymont D, Freemont Pet al., 2019, Rapid prototyping platform for Saccharomyces cerevisiae using computer-aided genetic design enabled by parallel software and workcell platform development, Slas Technology, Vol: 24, Pages: 291-297, ISSN: 2472-6303

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

McCarty NS, Shaw WM, Ellis T, Ledesma-Amaro Ret al., 2019, Rapid assembly of gRNA arrays via modular cloning in yeast, ACS Synthetic Biology, Vol: 8, Pages: 906-910, ISSN: 2161-5063

CRISPR is a versatile technology for genomic editing and regulation, but the expression of multiple gRNAs in S. cerevisiae has thus far been limited. We present here a simple extension to the Yeast MoClo Toolkit, which enables the rapid assembly of gRNA arrays using a minimal set of parts. Using a dual-PCR, Type IIs restriction enzyme Golden Gate assembly approach, at least 12 gRNAs can be assembled and expressed from a single transcriptional unit. We demonstrate that these gRNA arrays can stably regulate gene expression in a synergistic manner via dCas9-mediated repression. This approach expands the number of gRNAs that can be expressed in this model organism and may enable the versatile editing or transcriptional regulation of a greater number of genes in vivo.

Journal article

Boo A, Ellis T, Stan G, 2019, Host-aware synthetic biology, Current Opinion in Systems Biology, Vol: 14, Pages: 66-72, ISSN: 2452-3100

Unnatural gene expression imposes a load on engineered microorganisms thatdecreases their growth and subsequent production yields, a phenomenon knownasburden. In the last decade, the field of synthetic biology has made progress onthe development of biomolecular feedback control systems and other approachesthat can improve the growth of engineered cells, as well as the genetic stability,portability and robust performance of cell-hosted synthetic constructs. In thisreview, we highlight recent work focused on the development of host-aware syn-thetic biology.

Journal article

Stan G, Ellis T, Boo A, Host-Aware Synthetic Biology, Current Opinion in Systems Biology, ISSN: 2452-3100

Journal article

Shaw W, Yamauchi H, Mead J, Gowers G, Bell D, Oling D, Larsson N, Wigglesworth M, Ladds G, Ellis Tet al., Engineering a model cell for rational tuning of GPCR signaling, Cell, ISSN: 0092-8674

G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond tospecific cues in their environment. However, the relationship between stimulus and response for eachGPCR is difficult to predict due to diversity in natural signal transduction architecture and expression.Using genome engineering in yeast, we here constructed an insulated, modular GPCR signaltransduction system to study how the response to stimuli can be predictably tuned using synthetictools. We delineated the contributions of a minimal set of key components via computational andexperimental refactoring, identifying simple design principles for rationally tuning the dose-response.Using five different GPCRs, we demonstrate how this enables cells and consortia to be engineeredto respond to desired concentrations of peptides, metabolites, and hormones relevant to humanhealth. This work enables rational tuning of cell sensing, while providing a framework to guidereprogramming of GPCR-based signaling in other systems.

Journal article

Gilbert C, Ellis T, 2019, Biological engineered living materials - growing functional materials with genetically-programmable properties, ACS Synthetic Biology, Vol: 8, Pages: 1-15, ISSN: 2161-5063

Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair and the ability to sense-and-respond to environmental stimuli. Despite having found numerous uses in human industry and society, the utility of natural biological materials is limited. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection between microbiology, material science and synthetic biology, the emerging field of biological Engineered Living Materials (ELMs) aims to answer this question. Here we review recent efforts to program cells to produce living materials with novel functional properties, focussing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation that could be used to produce the more complex systems of the future.

Journal article

Weenink T, van der Hilst J, McKiernan R, Ellis Tet al., 2019, Design of RNA hairpin modules that predictably tune translation in yeast, Synthetic Biology, Vol: 3, ISSN: 2397-7000

Modular parts for tuning translation are prevalent in prokaryotic synthetic biology but lacking for eukaryotic synthetic biology. Working in Saccharomyces cerevisiae yeast, we here describe how hairpin RNA structures inserted into the 5′ untranslated region (5′UTR) of mRNAs can be used to tune expression levels by 100-fold by inhibiting translation. We determine the relationship between the calculated free energy of folding in the 5′UTR and in vivo protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this new tool, computational RNA sequence design can be used to predictably fine-tune protein production for genes expressed in yeast.

Journal article

Blount B, Ellis T, 2019, The Synthetic Genome Summer Course, Synthetic Biology, Vol: 3, ISSN: 2397-7000

The Synthetic Genome Summer Course was convened with the aim of teaching a wide range of researchers the theory and practical skills behind recent advances in synthetic biology and synthetic genome science, with a focus on Sc2.0, the synthetic yeast genome project. Through software workshops, tutorials and research talks from leading members of the field, the 30 attendees learnt about relevant principles and techniques that they were then able to implement first-hand in laboratory-based practical sessions. Participants SCRaMbLEd semi-synthetic yeast strains to diversify heterologous pathways, used automation to build combinatorial pathway libraries and used CRISPR to debug fitness defects caused by synthetic chromosome design changes. Societal implications of synthetic chromosomes were explored and industrial stakeholders discussed synthetic biology from a commercial standpoint. Over the 5 days, participants gained valuable insight and acquired skills to aid them in future synthetic genome research.

Journal article

Ellis T, 2019, Predicting how evolution will beat us, MICROBIAL BIOTECHNOLOGY, Vol: 12, Pages: 41-43, ISSN: 1751-7915

Journal article

Gorochowski TE, Ellis T, 2018, Designing efficient translation, NATURE BIOTECHNOLOGY, Vol: 36, Pages: 934-935, ISSN: 1087-0156

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

Shaw WM, Yamauchi H, Mead J, Gowers G-OF, Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis Tet al., 2018, Engineering a model cell for rational tuning of GPCR signaling, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:p>G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relationship between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, we here constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. We delineated the contributions of a minimal set of key components via computational and experimental refactoring, identifying simple design principles for rationally tuning the dose-response. Using four different receptors, we demonstrate how this enables cells and consortia to be engineered to respond to desired concentrations of peptides, metabolites and hormones relevant to human health. This work enables rational tuning of cell sensing, while providing a framework to guide reprogramming of GPCR-based signaling in more complex systems.</jats:p>

Working paper

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

Synthetic biology is maturing into a true engineering discipline for model microorganisms, but remains far from straightforward for most eukaryotes. Here, we outline the key challenges facing those trying to engineer biology across eukaryota and suggest areas of focus that will aid future progress.

Journal article

Blount B, Gowers G, Ho JCH, Ledesma-Amaro R, Jovicevic D, McKiernan R, Xie ZX, Li BZ, Yuan YJ, Ellis Tet al., 2018, Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome, Nature Communications, Vol: 9, ISSN: 2041-1723

Synthetic biology tools, such as modular parts and combinatorial DNA assembly, are routinely used to optimise the productivity of heterologous metabolic pathways for biosynthesis or substrate utilisation, yet, it is well established that host strain background is just as important for determining productivity. Here we report that in vivo combinatorial genomic rearrangement of Saccharomyces cerevisiae yeast with a synthetic chromosome V can rapidly generate new, improved host strains with genetic backgrounds favourable to diverse heterologous pathways, including those for violacein and penicillin biosynthesis and for xylose utilisation. We show how the modular rearrangement of synthetic chromosomes by SCRaMbLE can be easily determined using long-read nanopore sequencing and we explore experimental conditions that optimise diversification and screening. This new synthetic genome approach to metabolic engineering provides productivity improvements in a fast, simple and accessible way, making it a valuable addition to existing strain improvement techniques.

Journal article

Avalos JL, Toettcher JE, Lalanne J-B, Li G-W, Gomes ALC, Johns NI, Wang HH, Ellis T, Stan G-B, Mure LS, Panda S, Cooper HM, Fernandez-Martinez J, Rout MP, Akey CW, Kim SJ, Sali A, Bastarache L, Denny JCet al., 2018, Principles of Systems Biology, No. 28, CELL SYSTEMS, Vol: 6, Pages: 397-399, ISSN: 2405-4712

Journal article

Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan G, Ellis Tet al., 2018, Cell-free prediction of protein expression costs for growing cells, Nature Communications, Vol: 9, ISSN: 2041-1723

Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.

Journal article

Ceroni F, Boo A, Furini S, Gorochowski T, Ladak Y, Awan A, Gilbert C, Stan G, Ellis Tet al., 2018, Burden-driven feedback control of gene expression, Nature Methods, Vol: 15, Pages: 387-393, ISSN: 1548-7091

Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable.

Journal article

Pothoulakis G, Ellis T, 2018, Construction of hybrid regulated mother-specific yeast promoters for inducible differential gene expression, PLoS ONE, Vol: 13, ISSN: 1932-6203

Engineered promoters with predefined regulation are a key tool for synthetic biology that enable expression on demand and provide the logic for genetic circuits. To expand the availability of synthetic biology tools for S. cerevisiae yeast, we here used hybrid promoter engineering to construct tightly-controlled, externally-inducible promoters that only express in haploid mother cells that have contributed a daughter cell to the population. This is achieved by combining elements from the native HO promoter and from a TetR-repressible synthetic promoter, with the performance of these promoters characterized by both flow cytometry and microfluidics-based fluorescence microscopy. These new engineered promoters are provided as an enabling tool for future synthetic biology applications that seek to exploit differentiation within a yeast population.

Journal article

Pothoulakis G, Ellis T, 2018, Synthetic gene regulation for independent external induction of the Saccharomyces cerevisiae pseudohyphal growth phenotype, Communications Biology, Vol: 1, ISSN: 2399-3642

Pseudohyphal growth is a multicellular phenotype naturally performed by wild budding yeast cells in response to stress. Unicellular yeast cells undergo gross changes in their gene regulation and elongate to form branched filament structures consisting of connected cells. Here, we construct synthetic gene regulation systems to enable external induction of pseudohyphal growth in Saccharomyces cerevisiae. By controlling the expression of the natural PHD1 and FLO8 genes we are able to trigger pseudohyphal growth in both diploid and haploid yeast, even in different types of rich media. Using this system, we also investigate how members of the BUD gene family control filamentation in haploid cells. Finally, we employ a synthetic genetic timer network to control pseudohyphal growth and further explore the reversibility of differentiation. Our work demonstrates that synthetic regulation can exert control over a complex multigene phenotype and offers opportunities for rationally modifying the resulting multicellular structure.

Journal article

Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, Oheigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJet al., 2017, A transatlantic perspective on 20 emerging issues in biological engineering, eLife, Vol: 6, ISSN: 2050-084X

Advances in biological engineering are likely to have substantial impacts on global society. To explorethese potential impacts we ran a horizon scanning exercise to capture a range of perspectives on the opportunitiesand risks presented by biological engineering. We first identified 70 potential issues, and then used an iterativeprocess to prioritise 20 issues that we considered to be emerging, to have potential global impact, and to berelatively unknown outside the field of biological engineering. The issues identified may be of interest toresearchers, businesses and policy makers in sectors such as health, energy, agriculture and the environment.

Journal article

Mitchell LA, Ellis T, 2017, Synthetic genome engineering gets infectious, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 114, Pages: 11006-11008, ISSN: 0027-8424

Journal article

Jewett MC, Ellis T, 2017, Editorial overview: Synthetic biology: Frontiers in synthetic biology, CURRENT OPINION IN CHEMICAL BIOLOGY, Vol: 40, Pages: A1-A3, ISSN: 1367-5931

Journal article

Ceroni F, Furini S, Gorochowski T, Boo A, Borkowski O, Ladak Y, Awan A, Gilbert C, Stan G-B, Ellis Tet al., 2017, Burden-driven feedback control of gene expression, Publisher: Cold Spring Harbor Laboratory

Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable.

Working paper

Borkowski O, Bricio Garberi C, Murgiano M, Stan G-B, Ellis Tet al., 2017, Cell-free prediction of protein expression costs for growing cells, Publisher: bioRxiv

Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any gene is a major challenge, as multiple processes and factors determine translation efficiency. Here, to enable prediction of the cost of gene expression in bacteria, we describe a standard cell-free lysate assay that determines the relationship between in vivo and cell-free measurements and γ, a relative measure of the resource consumption when a given protein is expressed. When combined with a computational model of translation, this enables prediction of the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.

Working paper

Weenink T, McKiernan RM, Ellis T, 2017, Rational Design of RNA Structures that Predictably Tune Eukaryotic Gene Expression, Publisher: Cold Spring Harbor Laboratory

<jats:title>Abstract</jats:title><jats:p>Predictable tuning of gene expression is essential for engineering genetic circuits and for optimising enzyme levels in metabolic engineering projects. In bacteria, gene expression can be tuned at the stage of transcription, by exchanging the promoter, or at stage of translation by altering the ribosome binding site sequence. In eukaryotes, however, only promoter exchange is regularly used, as the tools to modulate translation are lacking. Working in <jats:italic>S. cerevisiae</jats:italic> yeast, we here describe how hairpin RNA structures inserted into the 5’ untranslated region (5’UTR) of mRNAs can be used to tune expression levels by altering the efficiency of translation initiation. We demonstrate a direct link between the calculated free energy of folding in the 5’UTR and protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and it outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this tool, computational RNA sequence design can be used to predictably fine-tune protein production, providing a new way to modulate gene expression in eukaryotes.</jats:p>

Working paper

Awan AR, Blount BA, Bell DJ, Shaw WM, Ho JCH, McKiernan RM, Ellis Tet al., 2017, Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast, Nature Communications, Vol: 8, ISSN: 2041-1723

Fungi are a valuable source of enzymatic diversity and therapeutic natural products includingantibiotics. Here we engineer the baker’s yeastSaccharomyces cerevisiaeto produce andsecrete the antibiotic penicillin, a beta-lactam nonribosomal peptide, by taking genes from afilamentous fungus and directing their efficient expression and subcellular localization. Usingsynthetic biology tools combined with long-read DNA sequencing, we optimize productivityby 50-fold to produce bioactive yields that allow spentS. cerevisiaegrowth media to haveantibacterial action againstStreptococcusbacteria. This work demonstrates thatS. cerevisiaecan be engineered to perform the complex biosynthesis of multicellular fungi, opening up thepossibility of using yeast to accelerate rational engineering of nonribosomal peptideantibiotics.

Journal article

Gilbert C, Howarth M, Harwood CR, Ellis Tet al., 2017, Extracellular self-assembly of functional and tunable protein conjugates from Bacillus subtilis, ACS Synthetic Biology, Vol: 6, Pages: 957-967, ISSN: 2161-5063

The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics, and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis. Using this approach, we demonstrate how self-conjugation of a secreted industrial enzyme, XynA, dramatically increases its resilience to boiling, and we show that cellular consortia can be engineered to self-assemble functional protein–protein conjugates with tunable composition. This novel genetically encoded modular system provides a flexible strategy for protein conjugation harnessing the substantial advantages of extracellular self-assembly.

Journal article

Ellis T, Cai Y, 2016, Synthetic Biology in Europe, ACS SYNTHETIC BIOLOGY, Vol: 5, Pages: 1033-1033, ISSN: 2161-5063

Journal article

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