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

106 results found

Walker K, Li IS, Lee K, Ellis Tet al., 2024, Self-pigmenting textiles grown from cellulose-producing bacteria with engineered tyrosinase expression, Nature Biotechnology, ISSN: 1087-0156

Journal article

Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Yet al., 2023, Design, construction, and functional characterization of a tRNA neochromosome in yeast, Cell, Vol: 186, Pages: 5237-5253.e22, ISSN: 0092-8674

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Journal article

Shaw WM, Khalil AS, Ellis T, 2023, A multiplex MoClo Toolkit for extensive and flexible engineering of Saccharomyces cerevisiae, ACS Synthetic Biology, Vol: 12, Pages: 3393-3405, ISSN: 2161-5063

Synthetic biology toolkits are one of the core foundations on which the field has been built, facilitating and accelerating efforts to reprogram cells and organisms for diverse biotechnological applications. The yeast Saccharomyces cerevisiae, an important model and industrial organism, has benefited from a wide range of toolkits. In particular, the MoClo Yeast Toolkit (YTK) enables the fast and straightforward construction of multigene plasmids from a library of highly characterized parts for programming new cellular behavior in a more predictable manner. While YTK has cultivated a strong parts ecosystem and excels in plasmid construction, it is limited in the extent and flexibility with which it can create new strains of yeast. Here, we describe a new and improved toolkit, the Multiplex Yeast Toolkit (MYT), that extends the capabilities of YTK and addresses strain engineering limitations. MYT provides a set of new integration vectors and selectable markers usable across common laboratory strains, as well as additional assembly cassettes to increase the number of transcriptional units in multigene constructs, CRISPR-Cas9 tools for highly efficient multiplexed vector integration, and three orthogonal and inducible promoter systems for conditional programming of gene expression. With these tools, we provide yeast synthetic biologists with a powerful platform to take their engineering ambitions to exciting new levels.

Journal article

Ellis T, Blount B, 2023, Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics, Cell Genomics, Vol: 3, ISSN: 2666-979X

We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.

Journal article

Peng H, Chen R, Shaw WM, Hapeta P, Jiang W, Bell DJ, Ellis T, Ledesma-Amaro Ret al., 2023, Modular metabolic engineering and synthetic coculture strategies for the production of aromatic compounds in yeast, ACS Synthetic Biology, Vol: 12, Pages: 1739-1749, ISSN: 2161-5063

Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. In this study, we used the model yeast Saccharomyces cerevisiae to produce aromatic molecules by exploiting the concept of modularity in synthetic biology. Three different modular approaches were investigated for the production of the valuable fragrance raspberry ketone (RK), found in raspberry fruits and mostly produced from petrochemicals. The first strategy used was modular cloning, which enabled the generation of combinatorial libraries of promoters to optimize the expression level of the genes involved in the synthesis pathway of RK. The second strategy was modular pathway engineering and involved the creation of four modules, one for product formation: RK synthesis module (Mod. RK); and three for precursor synthesis: aromatic amino acid synthesis module (Mod. Aro), p-coumaric acid synthesis module (Mod. p-CA), and malonyl-CoA synthesis module (Mod. M-CoA). The production of RK by combinations of the expression of these modules was studied, and the best engineered strain produced 63.5 mg/L RK from glucose, which is the highest production described in yeast, and 2.1 mg RK/g glucose, which is the highest yield reported in any organism without p-coumaric acid supplementation. The third strategy was the use of modular cocultures to explore the effects of division of labor on RK production. Two two-member communities and one three-member community were created, and their production capacity was highly dependent on the structure of the synthetic community, the inoculation ratio, and the culture media. In certain conditions, the cocultures outperformed their monoculture controls for RK production, although this was not the norm. Interestingly, the cocultures showed up to 7.5-fold increase and 308.4 mg/L of 4-hydroxy benzalacetone, the direct precursor of RK, which can be used for the semi-synthesis of RK. This study illustrates the utility of modularity in synth

Journal article

Xu X, Meier F, Blount BA, Pretorius IS, Ellis T, Paulsen IT, Williams TCet al., 2023, Trimming the genomic fat: minimising and re-functionalising genomes using synthetic biology, NATURE COMMUNICATIONS, Vol: 14

Journal article

Walker KT, Keane J, Goosens VJ, Song W, Lee K-Y, Ellis Tet al., 2023, Self-dyeing textiles grown from cellulose-producing bacteria with engineered tyrosinase expression

<jats:title>Abstract</jats:title><jats:p>Environmental concerns are driving interests in post-petroleum synthetic textiles produced from microbial and fungal sources. Bacterial cellulose is a promising sustainable leather alternative, on account of its material properties, low infrastructure needs and biodegradability. However, for alternative textiles like bacterial cellulose to be fully sustainable, alternative ways to dye textiles need to be developed alongside alternative production methods. To address this, we here use genetic engineering of<jats:italic>Komagataeibacter rhaeticus</jats:italic>to create a bacterial strain that grows self-dyeing bacterial cellulose. Dark black pigmentation robust to material use is achieved through melanin biosynthesis in the bacteria from recombinant tyrosinase expression. Melanated bacterial cellulose production can be scaled up for the construction of prototype fashion products, and we illustrate the potential of combining engineered self-dyeing with tools from synthetic biology, via the optogenetic patterning of gene expression in cellulose-producing bacteria. With this work, we demonstrate that combining genetic engineering with current and future methods of textile biofabrication has the potential to create a new class of textiles.</jats:p>

Journal article

Shaw WM, Studena L, Roy K, Hapeta P, McCarty NS, Graham AE, Ellis T, Ledesma-Amaro Ret al., 2023, Author Correction: Inducible expression of large gRNA arrays for multiplexed CRISPRai applications( doi 10.1038/s41467-022-32603-7, 25 augu , 20220, Nature Communications, Vol: 14, Pages: 1-1, ISSN: 2041-1723

Journal article

Caro-Astorga J, Lee K, Ellis T, 2022, Increasing bacterial cellulose compression resilience with glycerol or PEG400 as a route to more robust engineered living materials, Carbohydrate Polymer Technologies and Applications, Vol: 4, Pages: 1-6, ISSN: 2666-8939

Bacterial cellulose (BC) is one of the current natural materials at the edge of innovation in engineered living materials (ELMs) research due to its ease of growth and outstanding properties as a hydrogel. One of the main limitations of this material, however, is its quick dehydration in open environments as water molecules leave the porous network. Here we show that other solvents with higher evaporation temperatures, namely glycerol and polyethylene glycol (PEG), can play the same role as water within the BC structure interacting with cellulose fibres via hydrogen bonds. We demonstrate that these molecules provide up to a 130-fold improvement in the Young´s Modulus of BC hydrogels to compression forces in a concentration dependent manner. To take advantage of these effects for application in BC-based ELMs produced by Komagataeibacter rhaeticus, we also explored the effect of glycerol and PEG400 on the survival of the BC-producing bacteria in BC pieces. PEG400 at 20% doubled the material resilience to compression forces, still allowing bacteria to survive within the material for weeks. These results open further opportunities to explore new applications and stacked storage conditions.

Journal article

Shaw W, Lu X, Ellis T, 2022, Screening microbially produced Δ9-tetrahydrocannabinol using a yeast biosensor workflow, Nature Communications, Vol: 13, Pages: 1-10, ISSN: 2041-1723

Microbial production of cannabinoids promises to provide a consistent, cheaper, and more sustainable supply of these important therapeutic molecules. However, scaling production to compete with traditional plant-based sources is challenging. Our ability to make strain variants greatly exceeds our capacity to screen and identify high producers, creating a bottleneck in metabolic engineering efforts. Here, we present a yeast-based biosensor for detecting microbially produced Δ9-tetrahydrocannabinol (THC) to increase throughput and lower the cost of screening. We port five human cannabinoid G protein-coupled receptors (GPCRs) into yeast, showing the cannabinoid type 2 receptor, CB2R, can couple to the yeast pheromone response pathway and report on the concentration of a variety of cannabinoids over a wide dynamic and operational range. We demonstrate that our cannabinoid biosensor can detect THC from microbial cell culture and use this as a tool for measuring relative production yields from a library of Δ9-tetrahydrocannabinol acid synthase (THCAS) mutants.

Journal article

Ledesma Amaro R, Ellis T, Shaw W, Studena L, Roy K, Mccarty N, Graham A, Hapeta Pet al., 2022, Inducible expression of large gRNA arrays for multiplexed CRISPRai applications, Nature Communications, Vol: 13, ISSN: 2041-1723

CRISPR gene activation and inhibition (CRISPRai) has become a powerful synthetic tool for influencing the expression of native genes for foundational studies, cellular reprograming, and metabolic engineering. Here we develop a method for near leak-free, inducible expression of a polycistronic array containing up to 24 gRNAs from two orthogonal CRISPR/Cas systems to increase CRISPRai multiplexing capacity and target gene flexibility. To achieve strong inducibility, we created a technology to silence gRNA expression within the array in the absence of the inducer, since we found that long gRNA arrays for CRISPRai can express themselves even without promoter. Using this method, we create a highly tuned and easy-to-use CRISPRai toolkit in the industrially relevant yeast, Saccharomyces cerevisiae, establishing the first system to combine simultaneous activation and repression, large multiplexing capacity, and inducibility. We demonstrate this platform by targeting 11 genes in central metabolism in a single transformation, achieving a 45-fold increase in succinic acid, which could be precisely controlled in an inducible manner. Our method offers a highly effective way to regulate genes and rewire metabolism in yeast, with principles of gRNA array construction and inducibility that should extend to other chassis organisms.

Journal article

Caro-Astorga J, Ellis T, 2022, Self-healing through adhesion, NATURE CHEMICAL BIOLOGY, Vol: 18, Pages: 239-240, ISSN: 1552-4450

Journal article

Goosens V, Walker K, aragon S, Singh A, Senthivel V, Dekker L, Caro Astorga J, Buat M, Song W, Lee KY, Ellis Tet al., 2021, Komagataeibacter tool kit (KTK): a modular cloning system for multigene constructs and programmed protein secretion from cellulose producing bacteria, ACS Synthetic Biology, Vol: 10, Pages: 3422-3434, ISSN: 2161-5063

Bacteria proficient at producing cellulose are an attractive synthetic biology host for the emerging field of Engineered Living Materials (ELMs). Species from the Komagataeibacter genus produce high yields of pure cellulose materials in a short time with minimal resources, and pioneering work has shown that genetic engineering in these strains is possible and can be used to modify the material and its production. To accelerate synthetic biology progress in these bacteria, we introduce here the Komagataeibacter tool kit (KTK), a standardised modular cloning system based on Golden Gate DNA assembly that allows DNA parts to be combined to build complex multigene constructs expressed in bacteria from plasmids. Working in Komagataeibacter rhaeticus, we describe basic parts for this system, including promoters, fusion tags and reporter proteins, before showcasing how the assembly system enables more complex designs. Specifically, we use KTK cloning to reformat the Escherichia coli curli amyloid fibre system for functional expression in K. rhaeticus, and go on to modify it as a system for programming protein secretion from the cellulose producing bacteria. With this toolkit, we aim to accelerate modular synthetic biology in these bacteria, and enable more rapid progress in the emerging ELMs community.

Journal article

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., Eng Biol, Vol: 5, Pages: 51-59

After 2 decades of growth and success, synthetic biology has now become a mature field that is driving significant innovation in the bioeconomy and pushing the boundaries of the biomedical sciences and biotechnology. So what comes next? In this article, 10 technological advances are discussed that are expected and hoped to come from the next generation of research and investment in synthetic biology; from ambitious projects to make synthetic life, cell simulators and custom genomes, through to new methods of engineering biology that use automation, deep learning and control of evolution. The non-exhaustive list is meant to inspire those joining the field and looks forward to how synthetic biology may evolve over the coming decades.

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

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, ISSN: 2452-3100

Journal article

Zorzan I, Lopez 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, ISSN: 2452-3100

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

Caro-Astorga J, Walker KT, Ellis T, 2020, Bacterial cellulose spheroids as building blocks for 2D and 3D engineered living materials

<jats:title>Abstract</jats:title><jats:p>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 from millimetre-scale balls of cellulose occasionally produced by <jats:italic>Acetobacteriacea</jats:italic> species, which we call BC spheroids. We define a reproducible protocol to produce BC spheroids and demonstrate their potential for use as building blocks to grow ELMs in 2D and 3D shapes. These BC spheroids can be genetically functionalized and used as the method to make and grow patterned BC-based ELMs to design. We further demonstrate the use of BC spheroids for the repair and regeneration of BC materials, and measure the survival of the BC-producing bacteria in the material over time. This work forwards our understanding of BC spheroid formation and showcases their potential for creating and repairing engineered living materials.</jats:p>

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

<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

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