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
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91 results found

Di Blasi R, Zouein A, Ellis T, Ceroni Fet al., 2021, Genetic toolkits to design and build mammalian synthetic systems, Trends in Biotechnology, Vol: 39, Pages: 1004-1018, ISSN: 0167-7799

Construction of DNA-encoded programs is central to synthetic biology and the chosen method oftendetermines the time required to design and build constructs for testing. Here we describe and summarisekey features of the available toolkits for DNA construction for mammalian cells. We compare the differentcloning strategies based on their complexity and the time needed to generate constructs of different sizes,and we reflect on why Golden Gate toolkits now dominate due to their modular design. We look forward tofuture advances, including accessory packs to cloning toolkits that can facilitating editing, orthogonality,advanced regulation, and integration into synthetic chromosome construction.

Journal article

Gallup O, Ming H, Ellis T, 2021, Ten future challenges for synthetic biology, Engineering Biology, Vol: 5, Pages: 51-59, ISSN: 2398-6182

Journal article

Caro-Astorga J, Walker KT, Herrera N, Lee K-Y, Ellis Tet al., 2021, Bacterial cellulose spheroids as building blocks for 3D and patterned living materials and for regeneration., Nature Communications, Vol: 12, Pages: 1-9, ISSN: 2041-1723

Engineered living materials (ELMs) based on bacterial cellulose (BC) offer a promising avenue for cheap-to-produce materials that can be programmed with genetically encoded functionalities. Here we explore how ELMs can be fabricated in a modular fashion from millimetre-scale biofilm spheroids grown from shaking cultures of Komagataeibacter rhaeticus. Here we define a reproducible protocol to produce BC spheroids with the high yield bacterial cellulose producer K. rhaeticus and demonstrate for the first time their potential for their use as building blocks to grow ELMs in 3D shapes. Using genetically engineered K. rhaeticus, we produce functionalized BC spheroids and use these to make and grow patterned BC-based ELMs that signal within a material and can sense and report on chemical inputs. We also investigate the use of BC spheroids as a method to regenerate damaged BC materials and as a way to fuse together smaller material sections of cellulose and synthetic materials into a larger piece. This work improves our understanding of BC spheroid formation and showcases their great potential for fabricating, patterning and repairing ELMs based on the promising biomaterial of bacterial cellulose.

Journal article

Lu X, Ellis T, 2021, Self-replicating digital data storage with synthetic chromosomes, NATIONAL SCIENCE REVIEW, Vol: 8, ISSN: 2095-5138

Journal article

Gilbert C, Tang T-C, Ott W, Dorr B, Shaw W, Sun G, Lu T, Ellis Tet al., 2021, Living materials with programmable functionalities grown from engineered microbial co-cultures, Nature Materials, Vol: 20, Pages: 691-700, ISSN: 1476-1122

Biological systems assemble living materials that are autonomously patterned, can self-repair and can sense and respond to their environment. The field of engineered living materials aims to create novel materials with properties similar to those of natural biomaterials using genetically-engineered organisms. Here we describe an approach to fabricate functional bacterial cellulose-based living materials using a stable co-culture of Saccharomyces cerevisiae yeast and bacterial cellulose-producing Komagataeibacter rhaeticus bacteria. Yeast strains can be engineered to secrete enzymes into bacterial cellulose, generating autonomously grown catalytic materials and enabling DNA-encoded modification of bacterial cellulose bulk properties. Alternatively, engineered yeast can be incorporated within the growing cellulose matrix, creating living materials that can sense and respond to chemical and optical stimuli. This symbiotic culture of bacteria and yeast is a flexible platform for the production of bacterial cellulosed-based engineered living materials with potential applications in biosensing and biocatalysis.

Journal article

Zorzan I, López AR, Malyshava A, Ellis T, Barberis Met al., 2021, Synthetic designs regulating cellular transitions: Fine-tuning of switches and oscillators, Current Opinion in Systems Biology, Vol: 25, Pages: 11-26

Biological circuits are responsible for transitions between cellular states in a timely fashion. For example, stem cells switch from an undifferentiated (unstable) state to a differentiated (stable) state. Conversely, cell cycle and circadian clocks are completed through transitions among successive (stable) states, i.e. waves, with (unstable) states switching them at definite timing. These transitions irreversibly determine the biological response or fate of a cell, to commit to reversible switches or to generate periodic oscillations of its state. Here, we review synthetic circuits that, in silico and in vivo, allow a cell to ‘make a decision’, i.e. to select which state to reach, among multiple ones available, through definite network designs. Specifically, we propose and discuss the designs, and their constituents motifs, which we consider to be more prone to reprogram cell behaviour, and whose parameters can be fine-tuned through systems biology and tested experimentally through Synthetic Biology. For these designs, exploration of the parameter space and of the influence of (external) cellular signals – which modulate circuit parameters – allows for the prediction of the circuit's response and its consequent impact on cell fate.

Journal article

Liberante FG, Ellis T, 2021, From kilobases to megabases: Design and delivery of large DNA constructs into mammalian genomes, Current Opinion in Systems Biology, Vol: 25, Pages: 1-10

As DNA synthesis has become cheaper, it has made assembly of larger and larger genes possible. To fully realise this opportunity for a new era of synthetic biology in mammals, a number of gaps are beginning to be addressed in the design, synthesis, assembly and delivery of DNA constructs into large genomes. While current DNA design software is still inadequate for complex mammalian genomes, editing large bacterial artificial chromosomes is now easier. Newer viral technologies, such as herpes simplex virus, have been adapted for assembly of mammalian artificial chromosomes. Further advances in genome engineering, such as CRISPR- and Retron-based systems, will simplify targeted insertion of big DNA – all promising an exciting future for this field.

Journal article

Horby PW, Roddick A, Spata E, Staplin N, Emberson J, Pessoa-Amorim G, Brightling C, Prudon B, Chadwick D, Ustianowski A, Ashish A, Todd S, Yates B, Buttery R, Scott S, Maseda D, Baillie JK, Buch M, Chappell L, Day J, Faust SN, Jaki T, Jeffery K, Juszczak E, Lim WS, Montgomery A, Mumford A, Rowan K, Thwaites G, Mafham M, Haynes R, Landray MJ, Horby PW, Landray MJ, Baillie JK, Buch M, Chappell L, Day J, Faust SN, Haynes R, Jaki T, Jeffery K, Juszczak E, Lim WS, Mafham M, Montgomery A, Mumford A, Rowan K, Thwaites G, Sandercock P, Darbyshire J, DeMets D, Fowler R, Lalloo D, Roberts I, Wittes J, Horby P, Landray MJ, Haynes R, Fletcher L, Barton J, Basoglu A, Brown R, Brudlo W, Denis E, Howard S, McChlery G, Taylor K, Cui G, Goodenough B, King A, Lay M, Murray D, Stevens W, Wallendszus K, Welsh R, Crichton C, Davies J, Goldacre R, Harper C, Knight F, Latham-Mollart J, Mafham M, Nunn M, Salih H, Welch J, Campbell M, Pessoa-Amorim G, Peto L, Roddick A, Knott C, Wiles J, Bell JL, Emberson J, Juszczak E, Linsell L, Spata E, Staplin N, Bagley G, Cameron S, Chamberlain S, Farrell B, Freeman H, Kennedy A, Whitehouse A, Wilkinson S, Wood C, Reith C, Davies K, Halls H, Holland L, Wilson K, Howie L, Lunn M, Rodgers P, Barnard A, Beety J, Birch C, Brend M, Chambers E, Chappell L, Crawshaw S, Drake C, Duckles-Leech H, Graham J, Harman T, Harper H, Lock S, Lomme K, McMillan N, Nickson I, Ohia U, OKell E, Poustie V, Sam S, Sharratt P, Sheffield J, Slade H, Hoff WV, Walker S, Williamson J, De Soyza A, Dimitri P, Faust SN, Lemoine N, Minton J, Gilmour K, Pearson K, Armah C, Campbell D, Cate H, Priest A, Thomas E, Usher R, Johnson G, Logan M, Pratt S, Price A, Shirley K, Walton E, Williams P, Yelnoorkar F, Hanson J, Membrey H, Gill L, Oliver A, Das S, Murphy S, Sutu M, Collins J, Monaghan H, Unsworth A, Beddows S, Williams KB, Dowling S, Gibbons K, Pine K, Asghar A, Aubrey P, Jewell DB, Donaldson K, Skinner T, Luo J, Mguni N, Muzengi N, Pleass R, Wayman E, Coe A, Hicks J, Hough M, Levettet al., 2021, Azithromycin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial, The Lancet, Vol: 397, Pages: 605-612, ISSN: 0140-6736

BackgroundAzithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.MethodsIn this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospital with COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once per day by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatment groups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment and were twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants and local study staff were not masked to the allocated treatment, but all others involved in the trial were masked to the outcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.FindingsBetween April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) were eligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was 65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomly allocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall, 561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days (rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No

Journal article

Singh A, Walker K, Ledesma Amaro R, Ellis Tet al., 2020, Engineering bacterial cellulose by synthetic biology, International Journal of Molecular Sciences, Vol: 21, ISSN: 1422-0067

Synthetic biology is an advanced form of genetic manipulation that applies the principles of modularity and engineering design to reprogram cells by changing their DNA. Over the last decade, synthetic biology has begun to be applied to bacteria that naturally produce biomaterials, in order to boost material production, change material properties and to add new functionalities to the resulting material. Recent work has used synthetic biology to engineer several Komagataeibacter strains; bacteria that naturally secrete large amounts of the versatile and promising material bacterial cellulose (BC). In this review, we summarize how genetic engineering, metabolic engineering and now synthetic biology have been used in Komagataeibacter strains to alter BC, improve its production and begin to add new functionalities into this easy-to-grow material. As well as describing the milestone advances, we also look forward to what will come next from engineering bacterial cellulose by synthetic biology.

Journal article

Meng F, Ellis T, 2020, The second decade of synthetic biology: 2010-2020., Nature Communications, Vol: 11, Pages: 5174-5174, ISSN: 2041-1723

Synthetic biology is among the most hyped research topics this century, and in2010 it entered its teenage years. But rather than these being a problematictime, we’ve seen synthetic biology blossom and deliver many new technologiesand landmark achievements.

Journal article

Gowers G, Chee S, Bell D, Suckling L, Kern M, Tew D, McClymont D, Ellis Tet al., 2020, Improved betulinic acid biosynthesis using synthetic yeast chromosome recombination and semi-automated rapid LC-MS screening, Nature Communications, Vol: 11, ISSN: 2041-1723

Synthetic biology, genome engineering and directed evolution offer innumerable tools to expedite engineering of strains for optimising biosynthetic pathways. One of the most radical is SCRaMbLE, a system of inducible in vivo deletion and rearrangement of synthetic yeast chromosomes, diversifying the genotype of millions of Saccharomyces cerevisiae cells in hours. SCRaMbLE can yield strains with improved biosynthetic phenotypes but is limited by screening capabilities. To address this bottleneck, we combine automated sample preparation, an ultra-fast 84-second LC-MS method, and barcoded nanopore sequencing to rapidly isolate and characterise the best performing strains. Here, we use SCRaMbLE to optimise yeast strains engineered to produce the triterpenoid betulinic acid. Our semi-automated workflow screens 1,000 colonies, identifying and sequencing 12 strains with between 2- to 7-fold improvement in betulinic acid titre. The broad applicability of this workflow to rapidly isolate improved strains from a variant library makes this a valuable tool for biotechnology.

Journal article

Gilbert C, Tang T-C, Ott W, Dorr BA, Shaw WM, Sun GL, Lu TK, Ellis Tet al., 2019, Living materials with programmable functionalities grown from engineered microbial co-cultures, Publisher: Cold Spring Harbor Laboratory

<jats:title>ABSTRACT</jats:title><jats:p>Biological systems assemble tissues and structures with advanced properties in ways that cannot be achieved by man-made materials. Living materials self-assemble under mild conditions, are autonomously patterned, can self-repair and sense and respond to their environment. Inspired by this, the field of engineered living materials (ELMs) aims to use genetically-engineered organisms to generate novel materials. Bacterial cellulose (BC) is a biological material with impressive physical properties and low cost of production that is an attractive substrate for ELMs. Inspired by how plants build materials from tissues with specialist cells we here developed a system for making novel BC-based ELMs by addition of engineered yeast programmed to add functional traits to a cellulose matrix. This is achieved via a synthetic ‘symbiotic culture of bacteria and yeast’ (Syn-SCOBY) approach that uses a stable co-culture of<jats:italic>Saccharomyces cerevisiae</jats:italic>with BC-producing<jats:italic>Komagataeibacter rhaeticus</jats:italic>bacetria. Our Syn-SCOBY approach allows inoculation of engineered cells into simple growth media, and under mild conditions materials self-assemble with genetically-programmable functional properties in days. We show that co-cultured yeast can be engineered to secrete enzymes into BC, generating autonomously grown catalytic materials and enabling DNA-encoded modification of BC bulk material properties. We further developed a method for incorporating<jats:italic>S. cerevisiae</jats:italic>within the growing cellulose matrix, creating living materials that can sense chemical and optical inputs. This enabled growth of living sensor materials that can detect and respond to environmental pollutants, as well as living films that grow images based on projected patterns. This novel and robust Syn-SCOBY system empowers the sustainable production of B

Working paper

Gowers G-OF, Cameron SJS, Perdones-Montero A, Bell D, Chee SM, Kern M, Tew D, Ellis T, Takats Zet al., 2019, Off-colony screening of biosynthetic libraries by rapid laser-enabled mass spectrometry, ACS Synthetic Biology, Vol: 8, Pages: 2566-2575, ISSN: 2161-5063

Leveraging advances in DNA synthesis and molecular cloning techniques, synthetic biology increasingly makes use of large construct libraries to explore large design spaces. For biosynthetic pathway engineering the ability to screen these libraries for a variety of metabolites of interest is essential. If the metabolite of interest or the metabolic phenotype is not easily measurable, screening soon becomes a major bottleneck involving time-consuming culturing, sample preparation, and extraction. To address this, we demonstrate the use of automated Laser-Assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) - a form of ambient laser desorption ionisation mass spectrometry - to perform rapid mass spectrometry analysis direct from agar plate yeast colonies without sample preparation or extraction. We use LA-REIMS to assess production levels of violacein and betulinic acid directly from yeast colonies at a rate of 6 colonies per minute. We then demonstrate the throughput enabled by LA-REIMS by screening over 450 yeast colonies in under 4 hours, while simultaneously generating recoverable glycerol stocks of each colony in real-time. This showcases LA-REIMS as a pre-screening tool to complement downstream quantification methods such as LCMS. Through pre-screening several hundred colonies with LA-REIMS, we successfully isolate and verify a strain with a 2.5-fold improvement in betulinic acid production. Finally, we show that LA-REIMS can detect 20 out of a panel of 27 diverse biological molecules, demonstrating the broad applicability of LA-REIMS to metabolite detection. The rapid and automated nature of LA-REIMS makes this a valuable new technology to complement existing screening technologies currently employed in academic and industrial workflows.

Journal article

Gowers G-O, Vince O, Charles J-H, Klarenberg I, Ellis T, Edwards Aet al., 2019, Entirely off-grid and solar-powered DNA sequencing of microbial communities during an ice cap traverse expedition, Genes, Vol: 10, Pages: 1-10, ISSN: 2073-4425

Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth’s surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have significantly lowered the barrier to studying the microbial communities on icecaps, their use has led to a bias for data collection in the near vicinity of these institutions. Here, miniaturisation of a DNA sequencing lab suitable for off-grid metagenomic studies is demonstrated. Using human power alone, this lab was transported across Europe’s largest ice cap (Vatnajökull, Iceland) by ski and sledge. After 11 days of unsupported polar-style travel, a metagenomic study of a geothermal hot spring gorge was conducted on the remote northern edge of the ice cap. This tent-based metagenomic study resulted in over 24 h of Nanopore sequencing, powered by solar power alone. This study demonstrates the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition.

Journal article

Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan SC, Schloss JA, Stracquadanio G, Trefzer A, Bader JS, Church GM, Coelho CM, Efcavitch JW, Güell M, Mitchell LA, Nielsen AAK, Peck B, Smith AC, Stewart CN, Tekotte Het al., 2019, Technological challenges and milestones for writing genomes., Science, Vol: 366, Pages: 310-312, ISSN: 0036-8075

Engineering biology with recombinant DNA, broadly called synthetic biology, has progressed tremendously in the last decade, owing to continued industrialization of DNA synthesis, discovery and development of molecular tools and organisms, and increasingly sophisticated modeling and analytic tools. However, we have yet to understand the full potential of engineering biology because of our inability to write and test whole genomes, which we call synthetic genomics. Substantial improvements are needed to reduce the cost and increase the speed and reliability of genetic tools. Here, we identify emerging technologies and improvements to existing methods that will be needed in four major areas to advance synthetic genomics within the next 10 years: genome design, DNA synthesis, genome editing, and chromosome construction (see table). Similar to other large-scale projects for responsible advancement of innovative technologies, such as the Human Genome Project, an international, cross-disciplinary effort consisting of public and private entities will likely yield maximal return on investment and open new avenues of research and biotechnology.

Journal article

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

Ellis T, 2019, What is synthetic genomics anyway?, The Biochemist, Vol: 41, Pages: 6-9, ISSN: 0954-982X

You may have heard of synthetic genomics. This headline-grabbing, high-profile, big science topic is starting to emerge catalysed by the pioneering work of famous names in synthetic biology and biotechnology like George Church and Craig Venter. But what is synthetic genomics and what is it being used for? As a prominent researcher at a recent UK meeting said: “Is it just synthetic biology with bigger bits of DNA?” Well no, not quite…

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

Shaw W, Yamauchi H, Mead J, Gowers G, Bell D, Oling D, Larsson N, Wigglesworth M, Ladds G, Ellis Tet al., 2019, Engineering a model cell for rational tuning of GPCR signaling, Cell, Vol: 177, Pages: 782-796.e27, ISSN: 0092-8674

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 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 five different GPCRs, 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 other systems.

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, 2019, Host-Aware Synthetic Biology, Current Opinion in Systems Biology, ISSN: 2452-3100

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

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

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

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

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

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