Imperial College London


Faculty of EngineeringDepartment of Chemical Engineering

Reader in Biotechnology



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Publication Type

74 results found

Spice AJ, Aw R, Bracewell DG, Polizzi KMet al., 2020, Improving the reaction mix of a Pichia pastoris cell-free system using a design of experiments approach to minimise experimental effort, SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, Vol: 5, Pages: 137-144

Journal article

Gschwend FJ, Hennequin LM, Brandt-Talbot A, Bedoya-Lora F, Kelsall GH, Polizzi K, Fennell PS, Hallett JPet al., 2020, Towards an environmentally and economically sustainable biorefinery: heavy metal contaminated waste wood as a low-cost feedstock in a low-cost ionic liquid process, Green Chemistry, Vol: 22, Pages: 5032-5041, ISSN: 1463-9262

In the present study, we used a low-cost protic ionic liquid, 1-methylimidazolium chloride, to simultaneously fractionate heavy metal contaminated wood and extract the metals from the wood at elevated temperature and short reaction time. This treatment selectively dissolves the lignin and hemicellulose in the biomass, leaving a solid cellulose-rich pulp, while coordinating and extracting 80–100% of the metal species present in the wood in a one-pot process. The lignin stream was recovered from the liquor and the cellulose was hydrolysed and then fermented into ethanol. The ionic liquid was recycled 6 times and the metals were recovered from the liquor via electrodeposition. This is the first time that highly contaminated waste wood has been integrated into a process which does not produce a contaminated waste stream, but instead valorises the wood as a feedstock for renewable chemicals, materials and fuels, while efficiently recovering the metals, converting a toxic environmental hazard into a rich source of biorenewables. We have therefore used an otherwise problematic waste as a low-cost lignocellulsoic feedstock for a circular bioeconomy concept.

Journal article

Arpino JAJ, Polizzi KM, 2020, A modular method for directing protein self-assembly, ACS Synthetic Biology, Vol: 9, Pages: 993-1002, ISSN: 2161-5063

Proteins are versatile macromolecules with diverse structure, charge, and function. They are ideal building blocks for biomaterials for drug delivery, biosensing, or tissue engineering applications. Simultaneously, the need to develop green alternatives to chemical processes has led to renewed interest in multienzyme biocatalytic routes to fine, specialty, and commodity chemicals. Therefore, a method to reliably assemble protein complexes using protein-protein interactions would facilitate the rapid production of new materials. Here we show a method for modular assembly of protein materials using a supercharged protein as a scaffolding "hub" onto which target proteins bearing oppositely charged domains have been self-assembled. The physical properties of the material can be tuned through blending and heating and disassembly triggered using changes in pH or salt concentration. The system can be extended to the synthesis of living materials. Our modular method can be used to reliably direct the self-assembly of proteins using small charged tag domains that can be easily encoded in a fusion protein.

Journal article

Bui-Le L, Clarke CJ, Bröhl A, Brogan APS, Arpino JAJ, Polizzi KM, Hallett Jet al., 2020, Revealing the complexity of ionic liquid-protein interactions through a multi-technique investigation, Communications Chemistry, Vol: 3, ISSN: 2399-3669

Ionic liquids offer exciting possibilities for biocatalysis as solvent properties provide rare opportunities for customizable, energy-efficient bioprocessing. Unfortunately, proteins and enzymes are generally unstable in ionic liquids and several attempts have been made to explain why; however, a comprehensive understanding of the ionic liquid–protein interactions remains elusive. Here, we present an analytical framework (circular dichroism (CD), fluorescence, ultraviolet-visible (UV/Vis) and nuclear magnetic resonance (NMR) spectroscopies, and small-angle X-ray scattering (SAXS)) to probe the interactions, structure, and stability of a model protein (green fluorescent protein (GFP)) in a range (acetate, chloride, triflate) of pyrrolidinium and imidazolium salts. We demonstrate that measuring protein stability requires a similar holistic analytical framework, as opposed to single-technique assessments that provide misleading conclusions. We reveal information on site-specific ionic liquid–protein interactions, revealing that triflate (the least interacting anion) induces a contraction in the protein size that reduces the barrier to unfolding. Robust frameworks such as this are critical to advancing non-aqueous biocatalysis and avoiding pitfalls associated with single-technique investigations.

Journal article

Moore SJ, Lai H-E, Kelwick RJR, Chee SM, Bell DJ, Polizzi KM, Freemont PSet al., 2020, Correction to EcoFlex: a multifunctional MoClo kit for E. coli synthetic biology., ACS Synthetic Biology, ISSN: 2161-5063

It has been brought to our attention that the original article contains a typographical error within Figure 1B, part ii. One of the 4-bp overhangs reads “GGAC” and should instead be “GTAC”, as is consistent throughout the original manuscript and deposited AddGene sequences.

Journal article

Riangrungroj P, Polizzi KM, 2020, BeQuIK (Biosensor Engineered Quorum Induced Killing): designer bacteria for destroying recalcitrant biofilms., Microbial Biotechnology, Vol: 13, Pages: 311-314, ISSN: 1751-7915

This opinion piece describes a new design for the remediation of recalcitrant biofilms. It builds on previous work to develop engineered E. coli that recognize quorum sensing signals from pathogens in a biofilm and secrete toxins in response. To solve the challenge of dilute signalling molecules, we propose to use nanobodies and enzymes displayed on the surface of the cells to localize them to the biofilm and degrade the extracellular polymeric substances, thus creating a solution with better 'seek and destroy' capabilities.

Journal article

Spice AJ, Aw R, Bracewell DG, Polizzi KMet al., 2020, Synthesis and assembly of Hepatitis B virus-like particles in a Pichia pastoris cell-free system, Frontiers in Bioengineering and Biotechnology, Vol: 8, ISSN: 2296-4185

Virus-like particles (VLPs) are supramolecular protein assemblies with the potential for unique and exciting applications in synthetic biology and medicine. Despite the attention VLPs have gained thus far, considerable limitations still persist in their production. Poorly scalable manufacturing technologies and inconsistent product architectures continue to restrict the full potential of VLPs. Cell-free protein synthesis (CFPS) offers an alternative approach to VLP production and has already proven to be successful, albeit using extracts from a limited number of organisms. Using a recently developed Pichia pastoris-based CFPS system, we have demonstrated the production of the model Hepatitis B core antigen VLP as a proof-of-concept. The VLPs produced in the CFPS system were found to have comparable characteristics to those previously produced in vivo and in vitro. Additionally, we have developed a facile and rapid synthesis, assembly and purification methodology that could be applied as a rapid prototyping platform for vaccine development or synthetic biology applications. Overall the CFPS methodology allows far greater throughput, which will expedite the screening of optimal assembly conditions for more robust and stable VLPs. This approach could therefore support the characterization of larger sample sets to improve vaccine development efficiency.

Journal article

Riangrungroj P, Bever CS, Hammock BD, Polizzi KMet al., 2019, A label-free optical whole-cell Escherichia coli biosensor for the detection of pyrethroid insecticide exposure, Scientific Reports, Vol: 9, Pages: 1-9, ISSN: 2045-2322

There is a growing need for low-cost, portable technologies for the detection of threats to the environment and human health. Here we propose a label-free, optical whole-cell Escherichia coli biosensor for the detection of 3-phenoxybenzoic acid (3-PBA), a biomarker for monitoring human exposure to synthetic pyrethroid insecticides. The biosensor functions like a competitive ELISA but uses whole-cells surface displaying an anti-3-PBA VHH as the detection element. When the engineered cells are mixed with 3-PBA-protein conjugate crosslinking that can be visually detected occurs. Free 3-PBA in samples competes with these crosslinks, leading to a detectable change in the output. The assay performance was improved by coloring the cells via expression of the purple-blue amilCP chromoprotein and the VHH expression level was reduced to obtain a limit of detection of 3 ng/mL. The optimized biosensor exhibited robust function in complex sample backgrounds such as synthetic urine and plasma. Furthermore, lyophilization enabled storage of biosensor cells for at least 90 days without loss of functionality. Our whole-cell biosensor is simple and low-cost and therefore has potential to be further developed as a screening tool for monitoring exposure to pyrethroids in low-resource environments.

Journal article

Marques MPC, Boyd AS, Polizzi K, Szita Net al., 2019, Microfluidic devices towards personalized health and wellbeing, JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY, Vol: 94, Pages: 2412-2415, ISSN: 0268-2575

Journal article

Moya-Ramirez I, Kontoravdi K, Polizzi K, 2019, Low-cost and user-friendly biosensor to test the integrity of mRNA molecules suitable for field applications, Biosensors and Bioelectronics, Vol: 137, Pages: 199-206, ISSN: 0956-5663

The use of mRNA in biotechnology has expanded with novel applications such as vaccines and therapeutic mRNA delivery recently demonstrated. For mRNA to be used in patients, quality control assays will need to be routinely established. Currently, there is a gap between the highly sophisticated RNA integrity tests available and broader application of mRNA-based products by non-specialist users, e.g. in mass vaccination campaigns. Therefore, the aim of this work was to develop a low-cost biosensor able to test the integrity of a mRNA molecule with low technological requirements and easy end-user application. The biosensor is based on a bi-functional fusion protein, composed by the λN peptide that recognizes its cognate aptamer encoded on the 5’ end of the RNA under study and β-lactamase, which is able to produce a colorimetric response through a simple test. We propose two different mechanisms for signal processing adapted to two levels of technological sophistication, one based on spectrophotometric measurements and other on visual inspection. We show that the proposed λN-βLac chimeric protein specifically targets its cognate RNA aptamer, boxB, using both gel shift and biolayer interferometry assays. More importantly, the results presented confirm the biosensor performs reliably, with a wide dynamic range and a proportional response at different percentages of full-length RNA, even when gene-sized mRNAs were used. Thus, the features of the proposed biosensor would allow to end-users of products such as mRNA vaccines to test the integrity of the product before its application in a low-cost fashion, enabling a more reliable application of these products.

Journal article

Kotidis P, Jedrzejewski P, Sou SN, Sellick C, Polizzi K, Del Val IJ, Kontoravdi Cet al., 2019, Model-based optimization of antibody galactosylation in CHO cell culture, Biotechnology and Bioengineering, Vol: 116, Pages: 1612-1626, ISSN: 1097-0290

Exerting control over the glycan moieties of antibody therapeutics is highly desirable from a product safety and batch-to-batch consistency perspective. Strategies to improve antibody productivity may compromise quality, while interventions for improving glycoform distribution can adversely affect cell growth and productivity. Process design therefore needs to consider the trade-off between preserving cellular health and productivity while enhancing antibody quality. In this work, we present a modeling platform that quantifies the impact of glycosylation precursor feeding - specifically that of galactose and uridine - on cellular growth, metabolism as well as antibody productivity and glycoform distribution. The platform has been parameterized using an initial training data set yielding an accuracy of ±5% with respect to glycoform distribution. It was then used to design an optimized feeding strategy that enhances the final concentration of galactosylated antibody in the supernatant by over 90% compared with the control without compromising the integral of viable cell density or final antibody titer. This work supports the implementation of Quality by Design towards higher-performing bioprocesses.

Journal article

Aw R, Polizzi KM, 2019, Biosensor‐assisted engineering of a high‐yield Pichia pastoris cell‐free protein synthesis platform, Biotechnology and Bioengineering, Vol: 116, Pages: 656-666, ISSN: 0006-3592

Cell‐free protein synthesis (CFPS) has recently undergone a resurgence partly due to the proliferation of synthetic biology. The variety of hosts used for cell‐free extract production has increased, which harnesses the diversity of cellular biosynthetic, protein folding, and posttranslational modification capabilities available. Here we describe a CFPS platform derived from Pichia pastoris, a popular recombinant protein expression host both in academia and the biopharmaceutical industry. A novel ribosome biosensor was developed to optimize the cell extract harvest time. Using this biosensor we identified a potential bottleneck in ribosome content. Therefore, we undertook strain engineering to overexpress global regulators of ribosome biogenesis to increase in vitro protein production. CFPS extracts from the strain overexpressing FHL1 had a 3‐fold increase in recombinant protein yield compared to those from the wild‐type X33 strain. Furthermore, our novel CFPS platform can produce complex therapeutic proteins, as exemplified by the production of human serum albumin to a final yield of 48.1 μg mL‐1. Therefore, this work not only adds to the growing number of CFPS systems from diverse organisms, but also provides a blueprint for rapidly engineering new strains with increased productivity in vitro that could be applied to other organisms.

Journal article

Kylilis N, Riangrungroj P, Lai H-E, Salema V, Fernández LÁ, Stan G-B, Freemont PS, Polizzi KMet al., 2019, Whole-cell biosensor with tuneable limit of detection enables low-cost agglutination assays for medical diagnostic applications, ACS Sensors, Vol: 4, Pages: 370-378, ISSN: 2379-3694

Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date, the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design can detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straight-forward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanbodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites as well as routine medical testing and personalized medicine.

Journal article

Trantidou T, Dekker L, Polizzi K, Ces O, Elani Yet al., 2018, Functionalizing cell-mimetic giant vesicles with encapsulated bacterial biosensors, Interface Focus, Vol: 8, ISSN: 2042-8901

The design of vesicle microsystems as artificial cells (bottom-up synthetic biology) has traditionally relied on the incorporation of molecular components to impart functionality. These cell mimics have reduced capabilities compared with their engineered biological counterparts (top-down synthetic biology), as they lack the powerful metabolic and regulatory pathways associated with living systems. There is increasing scope for using whole intact cellular components as functional modules within artificial cells, as a route to increase the capabilities of artificial cells. In this feasibility study, we design and embed genetically engineered microbes (Escherichia coli) in a vesicle-based cell mimic and use them as biosensing modules for real-time monitoring of lactate in the external environment. Using this conceptual framework, the functionality of other microbial devices can be conferred into vesicle microsystems in the future, bridging the gap between bottom-up and top-down synthetic biology.

Journal article

Kylilis N, Riangrungroj P, Lai H-E, Salema V, Fernandez LA, Stan G-B, Freemont P, Polizzi Ket al., 2018, A low-cost biological agglutination assay for medical diagnostic applications, Publisher: American Chemical Society

Affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing are key in addressing challenges in the diagnosis of medical conditions and for improving global health in general. Ideally, POC diagnostic tests should be highly selective for the biomarker, user-friendly, have a flexible design architecture and a low cost of production. Here we developed a novel agglutination assay based on whole E. coli cells surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design as a new diagnostic platform by the detection of a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations supported using straight-forward design rules and a mathematical model. Finally, we re-engineer E. coli cells for the detection of a medically relevant biomarker by the display of two different antibodies against the human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for both field-testing in the developing world, emergency or disaster relief sites as well as routine medical testing and personalized medicine.

Working paper

Aw R, McKay P, Shattock R, Polizzi Ket al., 2018, A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization, Protein Expression and Purification, Vol: 149, Pages: 43-50, ISSN: 1046-5928

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

Journal article

Kylilis N, Tuza ZA, Stan G, Polizzi KMet al., 2018, Tools for engineering coordinated system behaviour in synthetic microbial consortia, Nature Communications, Vol: 9, ISSN: 2041-1723

Advancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software tool that automatically selects orthogonal communication channels. We use this approach to identify up to four orthogonal channels in silico, and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels is an enabling step that facilitates the design of synthetic consortia for applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation and spatial organisation.

Journal article

Freemont PS, Moore S, MacDonald J, Wienecke S, Ishwarbhai A, Tsipa A, Aw R, Kylilis N, Bell D, McCymont D, Jensen K, Polizzi K, Biedendieck Ret al., 2018, Rapid acquisition and model-based analysis of cell-free transcription-translation reactions from non-model bacteria, Proceedings of the National Academy of Sciences, Vol: 115, Pages: E4340-E4349, ISSN: 0027-8424

Native cell-free transcription–translation systems offer a rapid route to characterize the regulatory elements (promoters, transcription factors) for gene expression from nonmodel microbial hosts, which can be difficult to assess through traditional in vivo approaches. One such host, Bacillus megaterium, is a giant Gram-positive bacterium with potential biotechnology applications, although many of its regulatory elements remain uncharacterized. Here, we have developed a rapid automated platform for measuring and modeling in vitro cell-free reactions and have applied this to B. megaterium to quantify a range of ribosome binding site variants and previously uncharacterized endogenous constitutive and inducible promoters. To provide quantitative models for cell-free systems, we have also applied a Bayesian approach to infer ordinary differential equation model parameters by simultaneously using time-course data from multiple experimental conditions. Using this modeling framework, we were able to infer previously unknown transcription factor binding affinities and quantify the sharing of cell-free transcription–translation resources (energy, ribosomes, RNA polymerases, nucleotides, and amino acids) using a promoter competition experiment. This allows insights into resource limiting-factors in batch cell-free synthesis mode. Our combined automated and modeling platform allows for the rapid acquisition and model-based analysis of cell-free transcription–translation data from uncharacterized microbial cell hosts, as well as resource competition within cell-free systems, which potentially can be applied to a range of cell-free synthetic biology and biotechnology applications.

Journal article

Tomazou M, Barahona M, Polizzi K, Stan Get al., 2018, Computational re-design of synthetic genetic oscillators for independent amplitude and frequency modulation, Cell Systems, Vol: 6, Pages: 508-520.e5, ISSN: 2405-4712

To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allowindependent modulation of amplitude and period. This need is currently unmet. Here, we demonstratecomputationally how two classic genetic oscillators – the dual-feedback oscillator and the repressilator– can be re-designed to provide independent control of amplitude and period and improve tuneability,that is, a broad dynamic range of periods and amplitudes accessible through the input “dials”. Ourapproach decouples frequency and amplitude modulation by incorporating an orthogonal “sinkmodule” where the key molecular species are channelled for enzymatic degradation. This “sinkmodule” maintains fast oscillation cycles while alleviating the translational coupling between theoscillator’s transcription factors and output. We characterise the behaviour of our re-designedoscillators over a broad range of physiologically reasonable parameters, explain why this facilitatesbroader function and control, and provide general design principles for building synthetic geneticoscillators that are more precisely controllable.

Journal article

Elani Y, Trantidou T, Wylie D, Dekker L, Polizzi K, Law R, Ces Oet al., 2018, Constructing vesicle-based artificial cells with embedded living cells as organelle-like modules, Scientific Reports, Vol: 8, ISSN: 2045-2322

There is increasing interest in constructing artificial cells by functionalisinglipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limitedin comparison to their biologicalcounterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger syntheticcell assembly. Using microfluidic technologies to construct such hybrid systems, we demonstrate that the vesicle host and the encapsulated cell operate in concert. The external architecture of the vesicle shields the cell from toxic surroundings, whilethe cellacts as a bioreactor module that processes encapsulated feedstock which is further processedby a synthetic enzymatic cascadeco-encapsulated in the vesicle.

Journal article

Jonas FRH, Royle KE, Aw R, Stan G, Polizzi KMet al., 2018, Investigating the consequences of asymmetric endoplasmic reticulum inheritance in Saccharomyces cerevisiae under stress using a combination of single cell measurements and mathematical modelling, Synthetic and Systems Biotechnology, Vol: 3, Pages: 64-75, ISSN: 2405-805X

Adaptation allows organisms to maintain a constant internal environment, which is optimised for growth. The unfolded protein response (UPR) is an example of a feedback loop that maintains endoplasmic reticulum (ER) homeostasis, and is characteristic of how adaptation is often mediated by transcriptional networks. The more recent discovery of asymmetric division in maintaining ER homeostasis, however, is an example of how alternative non-transcriptional pathways can exist, but are overlooked by gold standard transcriptomic or proteomic population-based assays. In this study, we have used a combination of fluorescent reporters, flow cytometry and mathematical modelling to explore the relative roles of asymmetric cell division and the UPR in maintaining ER homeostasis. Under low ER stress, asymmetric division leaves daughter cells with an ER deficiency, necessitating activation of the UPR and prolonged cell cycle during which they can recover ER functionality before growth. Mathematical analysis of and simulation results from our mathematical model reinforce the experimental observations that low ER stress primarily impacts the growth rate of the daughter cells. These results demonstrate the interplay between homeostatic pathways and the importance of exploring sub-population dynamics to understand population adaptation to quantitatively different stresses.

Journal article

Heide C, Ces O, Polizzi K, Kontoravdi Cet al., 2018, Creating cell-free protein synthesis factories, Pharmaceutical Bioprocessing, ISSN: 2048-9145

Journal article

Lai H-E, Moore S, Polizzi K, Freemont Pet al., 2018, EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology., Pages: 429-444

Development of advanced synthetic biology tools is always in demand since they act as a platform technology to enable rapid prototyping of biological constructs in a high-throughput manner. EcoFlex is a modular cloning (MoClo) kit for Escherichia coli and is based on the Golden Gate principles, whereby Type IIS restriction enzymes (BsaI, BsmBI, BpiI) are used to construct modular genetic elements (biological parts) in a bottom-up approach. Here, we describe a collection of plasmids that stores various biological parts including promoters, RBSs, terminators, ORFs, and destination vectors, each encoding compatible overhangs allowing hierarchical assembly into single transcription units or a full-length polycistronic operon or biosynthetic pathway. A secondary module cloning site is also available for pathway optimization, in order to limit library size if necessary. Here, we show the utility of EcoFlex using the violacein biosynthesis pathway as an example.

Book chapter

Kylilis N, Stan G-B, Polizzi K, 2017, Tools for engineering coordinated system behaviour in synthetic microbial consortia, Publisher: bioRxiv

Advancing synthetic biology to the multicellular level requires the development of multiple orthogonal cell-to-cell communication channels to propagate information with minimal signal interference. The development of quorum sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on reducing signal leakage between systems of cognate AHL/transcription factor pairs. However, the use of non-cognate signals as a design feature has received limited attention so far. Here, we demonstrate the largest library of AHL-receiver devices constructed to date with all cognate and non-cognate chemical signal interactions quantified and we develop a software tool that allows automated selection of orthogonal chemical channels. We use this approach to identify up to four orthogonal channels in silico and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels will facilitate the design of synthetic microbial consortia for novel applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation, and spatial organisation.

Working paper

Royle KE, Polizzi KM, 2017, A streamlined cloning workflow minimising the time-to-strain pipeline for Pichia pastoris, Scientific Reports, Vol: 7, ISSN: 2045-2322

Although recent advances in E. coli self-assembly have greatly simplified cloning, these have not yet been harnessed for the high-throughput generation of expression strains in the early research and discovery phases of biopharmaceutical production. Here, we have refined the technique and incorporated it into a streamlined workflow for the generation of Pichia pastoris expression strains, reducing the timeline by a third and removing the reliance on DNA editing enzymes, which often require troubleshooting and increase costs. We have validated the workflow by cloning 24 human proteins of biopharmaceutical value, either as direct therapeutics or as research targets, which span a continuous range in size and GC content. This includes demonstrating the applicability of the workflow to three-part assemblies for a monoclonal antibody and its single-chain antibody fragments derivatives. This workflow should enable future research into recombinant protein production by P. pastoris and a synthetic biology approach to this industrial host.

Journal article

Ogonah OW, Polizzi KM, Bracewell DG, 2017, Cell free protein synthesis: a viable option for stratified medicines manufacturing?, CURRENT OPINION IN CHEMICAL ENGINEERING, Vol: 18, Pages: 77-83, ISSN: 2211-3398

Journal article

Anastasiadi M, Polizzi K, Lambert RJW, 2017, An improved model for the analysis of combined antimicrobials: a replacement for the Chou-Talalay combination index method, Journal of Applied Microbiology, Vol: 124, Pages: 97-107, ISSN: 1364-5072

AIMS: To rationalise confusion in the literature concerning the analysis of combined antimicrobials, specifically to see if the combination index (CI) method of analysis was as rigorous as claimed. METHODS & RESULTS: data from previous studies of the inhibition of Staphylococcus aureus by mixed antimicrobials were re-analysed using the CI method and a model which takes account of differences in the concentration exponents of individual antimicrobials. CONCLUSIONS: The Chou-Talalay combination index method for the analysis of combined antimicrobials was found to be valid only in the specific cases where concentration exponents were equal. In these cases the CI method was found to be a function of the residuals of fitting the additive model to the observed data. Where concentration exponents were not equal the CI method was invalid, whereas the additive model took these differences into account. SIGNIFICANCE AND IMPACT OF STUDY: The CI method can be replaced wholly by the additive model described. The model allows simple regression to be used to analyse whole data sets and provides simple graphical output. This article is protected by copyright. All rights reserved.

Journal article

Sou SN, Ken L, Nayyar K, Polizzi KM, Sellick C, Kontoravdi Cet al., 2017, Exploring cellular behaviour under transient geneexpression and its impact on mAb productivity and Fc glycosylation, Biotechnology and Bioengineering, Vol: 115, Pages: 512-518, ISSN: 1097-0290

Transient gene expression (TGE) is a methodology employed in bioprocessing for the fast provision of recombinant protein material. Mild hypothermia is often introduced to overcome the low yield typically achieved with TGE and improve specific protein productivity. It is therefore of interest to examine the impact of mild hypothermic temperatures on both the yield and quality of transiently-expressed proteins and the relationship to changes in cellular processes and metabolism. In this study, we focus on the ability of a Chinese hamster ovary cell line to galactosylate a recombinant monoclonal antibody (mAb) product. Through experimentation and flux balance analysis, our results show that TGE in mild hypothermic conditions led to a 76% increase in qP compared to TGE at 36.5°C in our system. This increase is accompanied by increased consumption of nutrients and amino acids, together with increased production of intracellular nucleotide sugar species and higher rates of mAb galactosylation, despite a reduced rate of cell growth. The reduction in biomass accumulation allowed cells to redistribute their energy and resources towards mAb synthesis and Fc-glycosylation. Interestingly, the higher capacity of cells to galactosylate the recombinant product in TGE at 32°C appears not to have been assisted by the upregulation of galactosyltransferases (GalTs), but by the increased expression of N-acetylglucosaminyltransferase II (GnTII) in this cell line, which facilitated the production of bi-antennary glycan structures for further processing.

Journal article

Dekker L, Polizzi KM, 2017, Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors., Current Opinion in Chemical Biology, Vol: 40, Pages: 31-36, ISSN: 1367-5931

Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include multiplexed detection using microfluidics. Synthetic biology can be used to engineer new biological biosensors with improved characteristics. Although there have been few biosensors developed for bioprocessing thus far, emerging trends can be applied in the future. A range of new platform technologies will enable rapid engineering of new biosensors based on transcriptional activation, riboswitches, and Förster Resonance Energy Transfer. However, translation to industry remains a challenge and more research into the robustness biosensors at scale is needed.

Journal article

Goers L, Ainsworth C, Goey CH, Kontoravdi C, Freemont PS, Polizzi KMet al., 2017, Cover Image, Volume 114, Number 6, June 2017.

Cover Legend The cover image, by Lisa Goers et al., is based on the Article Whole-cell Escherichia coli lactate biosensor for monitoring mammalian cell cultures during biopharmaceutical production, DOI: 10.1002/bit.26254.


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