Publications
47 results found
Benton J, Jimenez Zarco J, Banks A, et al., 2024, Using microbes to remove microplastics from wastewater and sewage sludge, London, Publisher: Institute for Molecular Science and Engineering, Briefing paper No. 11
Microplastics are a widespread form of plastic pollution. There is increasing evidence that they are a threat to human health and the environment. Microplastics in domestic and industrial wastewater become concentrated in sewage sludge during wastewater treatment processes. In 2020, water companies in England produced more than 800,000 tonnes of sewage sludge from urban wastewater. More than 90% of UK sewage sludge is spread on agricultural land as a fertilizer and soil conditioner. This provides a pathway for microplastics to enter the terrestrial environment. There is currently no UK legislation defining safe limits for microplastics in sludge and soils but future regulation is a possibility. There is currently no technology available to remove microplastics from wastewater treatment processes or the resulting sludge. Safe limits for microplastics in treated sewage sludge, soils and water bodies should be identified. This will require a survey of the extent of microplastic pollution throughout the UK, including concentration, identity and characteristics of microplastics in each environmental reservoir, and understanding how microplastics affect different living organisms. Microbes or fungi that break down plastic could be added to existing wastewater treatment process to remove microplastics and prevent their release into the environment. Alternatively, only the active enzymes (rather than the live microorganisms) could be added to the process. Currently, only polyester microplastics (11% of the total microplastic burden) could be treated in this way. Different microorganisms would have to be discovered or developed to tackle other common microplastic polymers such as polypropylene or polyethylene.
Merali N, Chouari T, Terroire J, et al., 2023, Bile microbiome signatures associated with pancreatic ductal adenocarcinoma compared to benign disease: a UK pilot study, International Journal of Molecular Sciences, Vol: 24, ISSN: 1422-0067
Pancreatic ductal adenocarcinoma (PDAC) has a very poor survival. The intra-tumoural microbiome can influence pancreatic tumourigenesis and chemoresistance and, therefore, patient survival. The role played by bile microbiota in PDAC is unknown. We aimed to define bile microbiome signatures that can effectively distinguish malignant from benign tumours in patients presenting with obstructive jaundice caused by benign and malignant pancreaticobiliary disease. Prospective bile samples were obtained from 31 patients who underwent either Endoscopic Retrograde Cholangiopancreatography (ERCP) or Percutaneous Transhepatic Cholangiogram (PTC). Variable regions (V3-V4) of the 16S rRNA genes of microorganisms present in the samples were amplified by Polymerase Chain Reaction (PCR) and sequenced. The cohort consisted of 12 PDAC, 10 choledocholithiasis, seven gallstone pancreatitis and two primary sclerosing cholangitis patients. Using the 16S rRNA method, we identified a total of 135 genera from 29 individuals (12 PDAC and 17 benign). The bile microbial beta diversity significantly differed between patients with PDAC vs. benign disease (Permanova p = 0.0173). The separation of PDAC from benign samples is clearly seen through unsupervised clustering of Aitchison distance. We found three genera to be of significantly lower abundance among PDAC samples vs. benign, adjusting for false discovery rate (FDR). These were Escherichia (FDR = 0.002) and two unclassified genera, one from Proteobacteria (FDR = 0.002) and one from Enterobacteriaceae (FDR = 0.011). In the same samples, the genus Streptococcus (FDR = 0.033) was found to be of increased abundance in the PDAC group. We show that patients with obstructive jaundice caused by PDAC have an altered microbiome composition in the bile compared to those with benign disease. These bile-based microbes could be developed into potential diagnostic and prognostic biomarkers for PDAC and warrant further investigation.
Dvorak P, Galvao TC, Pflueger-Grau K, et al., 2023, Water potential governs the effector specificity of the transcriptional regulator XylR of Pseudomonas putida, Environmental Microbiology, Vol: 25, Pages: 1041-1054, ISSN: 1462-2912
The biodegradative capacity of bacteria in their natural habitats is affected by water availability. In this work, we have examined the activity and effector specificity of the transcriptional regulator XylR of the TOL plasmid pWW0 of Pseudomonas putida mt-2 for biodegradation of m-xylene when external water potential was manipulated with polyethylene glycol PEG8000. By using non-disruptive luxCDEAB reporter technology, we noticed that the promoter activated by XylR (Pu) restricted its activity and the regulator became more effector-specific towards head TOL substrates when cells were grown under water subsaturation. Such a tight specificity brought about by water limitation was relaxed when intracellular osmotic stress was counteracted by the external addition of the compatible solute glycine betaine. With these facts in hand, XylR variants isolated earlier as effector-specificity responders to the non-substrate 1,2,4-trichlorobenzene under high matric stress were re-examined and found to be unaffected by water potential in vivo. All these phenomena could be ultimately explained as the result of water potential-dependent conformational changes in the A domain of XylR and its effector-binding pocket, as suggested by AlphaFold prediction of protein structures. The consequences of this scenario for the evolution of specificities in regulators and the emergence of catabolic pathways are discussed.
Avendano R, Munoz-Montero S, Rojas-Gatjens D, et al., 2023, Production of selenium nanoparticles occurs throughan interconnected pathway of sulphur metabolism andoxidative stress response in Pseudomonas putida KT2440, Microbial Biotechnology, Vol: 16, Pages: 931-946, ISSN: 1751-7907
The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.
Fokialakis N, De la Calle F, Walshe K, et al., 2022, Sustainable Exploitation of Bio-Engineered Microorganisms for the Discovery and Development of Novel Biosurfactants and Siderophores with Industrial Applications, Publisher: GEORG THIEME VERLAG KG, Pages: 1466-1467, ISSN: 0032-0943
Fernandez-Gonzalez A, Cowen S, Kim J, et al., 2022, Applicability of control materials to support gene promoter characterization and expression in engineered cells using digital PCR, Analytical Chemistry, Vol: 94, Pages: 5566-5574, ISSN: 0003-2700
The use of standardized components and processes in engineering underpins the design-build-test model, and the engineering of biological systems is no different. Substantial efforts to standardize both the components and the methods to validate the engineered biological systems is ongoing. This study has developed a panel of control materials encoding the commonly used reporter genes GFP and RFP as DNA or RNA molecules. Each panel contained up to six samples with increasingly small copy number differences between the two reporter genes that ranged from 1- to 2-fold differences. These copy number differences represent the magnitude of changes that may need to be measured to validate an engineered system. Using digital PCR (dPCR), we demonstrated that it is possible to quantify changes in both gene and gene transcript numbers both within and between samples down to 1.05-fold. We corroborated these findings using a simple gene circuit within a bacterial model to demonstrate that dPCR was able to precisely identify small changes in gene expression of two transcripts in response to promoter stimulation. Finally, we used our findings to highlight sources of error that can contributed to the measurement uncertainty in the measurement of small ratios in biological systems. Together, the development of a panel of control materials and validation of a high accuracy method for the measurement of small changes in gene expression, this study can contribute to the engineering biology “toolkit” of methods and materials to support the current standardization efforts.
Hidalgo D, Martinez-Ortiz CA, Palsson BO, et al., 2022, Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity, iScience, Vol: 25, ISSN: 2589-0042
Bacteria regulate their cellular resource allocation to enable fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth, and expression profiles of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with only three of the seven copies of ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied fast-growing rpoB mutants. Comparing these two different regulatory perturbations (rRNA promoters or rpoB mutations), we show how they reshape the proteome for growth with a concomitant fitness cost. The fast-growing mutants shared downregulation of hedging functions and upregulated growth functions. They showed longer diauxic shifts and reduced activity of gluconeogenic promoters during glucose-acetate shifts, suggesting reduced availability of the RNA polymerase for expressing hedging proteome. These results show that the regulation of ribosomal allocation underlies the growth/hedging phenotypes obtained from laboratory evolution experiments.
Merali N, Chouari T, Kayani K, et al., 2022, A comprehensive review of the current and future role of the microbiome in pancreatic ductal adenocarcinoma, Cancers, Vol: 14, Pages: 1-34, ISSN: 2072-6694
Pancreatic ductal adenocarcinoma (PDAC) is expected to become the second most common cause of cancer death in the USA by 2030, yet progress continues to lag behind that of other cancers, with only 9% of patients surviving beyond 5 years. Long-term survivorship of PDAC and improving survival has, until recently, escaped our understanding. One recent frontier in the cancer field is the microbiome. The microbiome collectively refers to the extensive community of bacteria and fungi that colonise us. It is estimated that there is one to ten prokaryotic cells for each human somatic cell, yet, the significance of this community in health and disease has, until recently, been overlooked. This review examines the role of the microbiome in PDAC and how it may alter survival outcomes. We evaluate the possibility of employing microbiomic signatures as biomarkers of PDAC. Ultimately this review analyses whether the microbiome may be amenable to targeting and consequently altering the natural history of PDAC.
Vieto S, Rojas-Gatjens D, Jimenez JI, et al., 2021, The potential of <i>Pseudomonas</i> for bioremediation of oxyanions, ENVIRONMENTAL MICROBIOLOGY REPORTS, Vol: 13, Pages: 773-789, ISSN: 1758-2229
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- Citations: 6
Narancic T, Salvador M, Hughes GM, et al., 2021, Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates, Microbial Biotechnology, Vol: 14, Pages: 2463-2480, ISSN: 1751-7907
The throwaway culture related to the single-use materials such as polyethylene terephthalate (PET) has created a major environmental concern. Recycling of PET waste into biodegradable plastic polyhydroxyalkanoate (PHA) creates an opportunity to improve resource efficiency and contribute to a circular economy. We sequenced the genome of Pseudomonas umsongensis GO16 previously shown to convert PET-derived terephthalic acid (TA) into PHA and performed an in-depth genome analysis. GO16 can degrade a range of aromatic substrates in addition to TA, due to the presence of a catabolic plasmid pENK22. The genetic complement required for the degradation of TA via protocatechuate was identified and its functionality was confirmed by transferring the tph operon into Pseudomonas putida KT2440, which is unable to utilise TA naturally. We also identified the genes involved in ethylene glycol (EG) metabolism, the second PET monomer, and validated the capacity of GO16 to use EG as a sole source of carbon and energy. Moreover, GO16 possesses genes for the synthesis of both medium and short chain length PHA and we have demonstrated the capacity of the strain to convert mixed TA and EG into PHA. The metabolic versatility of GO16 highlights the potential of this organism for biotransformations using PET waste as a feedstock.
Hidalgo D, Martínez-Ortiz CA, Palsson BO, et al., 2021, Regulatory perturbations of ribosome allocation reshape the growth proteome with a trade-off in adaptation capacity
<jats:title>Summary</jats:title><jats:p>Bacteria regulate their cellular resource allocation to enable fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profiles of two sets of fast-growing mutants of <jats:italic>Escherichia coli</jats:italic> K-12 MG1655 in glucose minimal medium. Mutants with only 3 of the seven copies of ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied <jats:italic>rpoB</jats:italic> mutants. Higher growth rates due to increased ribosome content affected resource allocation. Expression profiles of fast-growing mutants shared downregulation of hedging functions and upregulated growth functions. Mutants showed longer diauxic shifts and reduced activity of gluconeogenic promoters during glucose-acetate shifts, suggesting reduced availability of the RNA Polymerase for expressing hedging proteome. These results show that the regulation of ribosomal allocation underlies the growth/hedging phenotypes obtained from laboratory evolution experiments. We show how two different regulatory perturbations (rRNA promoters or <jats:italic>rpoB</jats:italic> mutations) reshape the proteome for growth with a concomitant fitness cost</jats:p><jats:sec><jats:title>Highlights</jats:title><jats:p>Mutants with only 3 ribosomal operons grow faster than wild-type in minimal medium</jats:p><jats:p>Δ4 <jats:italic>rrn</jats:italic> and <jats:italic>rpoB</jats:italic> mutants share phenotypic traits</jats:p><jats:p>Faster growth of mutants is achieved by increased ribosome content</jats:p><jats:p>Fast-growing mutants display reduced hedging expression and adaptation trade-offs</jats:p><jats:p>Despite similar ribosomal content in rich medium the mutants present growth def
Kim J, Darlington APS, Bates DG, et al., 2021, The interplay between growth rate and nutrient quality defines gene expression capacity
<jats:title>Abstract</jats:title><jats:p>The gene expression capacity of bacterial cells depends on the interplay between growth and the availability of the transcriptional and translational machinery. Growth rate is widely accepted as the global physiological parameter controlling the allocation of cell resources. This allocation has an impact on the ability of the cell to produce both host and heterologous proteins required for synthetic circuits and pathways. Understanding the relationship between growth and resources is key for the efficient design of artificial genetic constructs, however, it is obscured by the mutual dependence of growth and gene expression on each other. In this work, we investigate the individual contributions of molecular factors, growth rate and metabolism to gene expression by investigating the behaviour of bacterial cells growing in chemostats in growth-limited conditions. We develop a model of the whole cell that captures trade-offs in gene expression arising from the individual contributions of different factors, and validate it by analysing gene couplings which emerge from competition for the gene expression machinery. Our results show that while growth rate and molecular factors, such as the number of rRNA operons, set the abundance of transcriptional and translational machinery available, it is metabolism that governs the usage of those resources by tuning elongation rates. We show that synthetic gene expression capacity can be maximised by using low growth in a high-quality medium. These findings provide valuable insights into fundamental trade-offs in microbial physiology that will inform future strain and bioprocesses optimisation.</jats:p>
González J, Salvador M, Özkaya Ö, et al., 2020, The loss of the pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion, The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 15, Pages: 1330-1343, ISSN: 1751-7362
The rapid emergence of antibiotic resistant bacterial pathogens constitutes a critical problem in healthcare and requires the development of novel treatments. Potential strategies include the exploitation of microbial social interactions based on public goods, which are produced at a fitness cost by cooperative microorganisms, but can be exploited by cheaters that do not produce these goods. Cheater invasion has been proposed as a ‘Trojan horse’ approach to infiltrate pathogen populations with strains deploying built-in weaknesses (e.g., sensitiveness to antibiotics). However, previous attempts have been often unsuccessful because population invasion by cheaters was prevented by various mechanisms including the presence of spatial structure (e.g., growth in biofilms), which limits the diffusion and exploitation of public goods. Here we followed an alternative approach and examined whether the manipulation of public good uptake and not its production could result in potential ‘Trojan horses’ suitable for population invasion. We focused on the siderophore pyoverdine produced by the human pathogen Pseudomonas aeruginosa MPAO1 and manipulated its uptake by deleting and/or overexpressing the pyoverdine primary (FpvA) and secondary (FpvB) receptors. We found that receptor synthesis feeds back on pyoverdine production and uptake rates, which led to strains with altered pyoverdine-associated costs and benefits. Moreover, we found that the receptor FpvB was advantageous under iron-limited conditions but revealed hidden costs in the presence of an antibiotic stressor (gentamicin). As a consequence, FpvB mutants became the fittest strain under gentamicin exposure, displacing the wildtype in liquid cultures, and in biofilms and during infections of the wax moth larvae Galleria mellonella, which both represent structured environments. Our findings reveal that an evolutionary trade-off associated with the costs and benefits of a versatile pyoverdine uptake
Lastiri-Pancardo G, Mercado-Hernandez JS, Kim J, et al., 2020, A quantitative method for proteome reallocation using minimal regulatory interventions (Jul, 10.1038/s41589-020-0593-y, 2020), NATURE CHEMICAL BIOLOGY, Vol: 16, Pages: 1277-1277, ISSN: 1552-4450
Lastiri-Pancardo G, Mercado-Hernandez JS, Kim J, et al., 2020, A quantitative method for proteome reallocation using minimal regulatory interventions, NATURE CHEMICAL BIOLOGY, Vol: 16, ISSN: 1552-4450
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- Citations: 19
González J, Salvador M, Özkaya Ö, et al., 2020, The loss of the pyoverdine secondary receptor in <i>Pseudomonas aeruginosa</i> results in a fitter strain suitable for population invasion
<jats:title>Abstract</jats:title><jats:p>The rapid emergence of antibiotic resistant bacterial pathogens constitutes a critical problem in healthcare and requires the development of novel treatments. Potential strategies include the exploitation of microbial social interactions based on public goods, which are produced at a fitness cost by cooperative microorganisms, but can be exploited by cheaters that do not produce these goods. Cheater invasion has been proposed as a ‘Trojan horse’ approach to infiltrate pathogen populations with strains deploying built-in weaknesses (e.g. sensitiveness to antibiotics). However, previous attempts have been often unsuccessful because population invasion by cheaters was prevented by various mechanisms including the presence of spatial structure (e.g. growth in biofilms), which limits the diffusion and exploitation of public goods. Here we followed an alternative approach and examined whether the manipulation of public good uptake and not its production could result in potential ‘Trojan horses’ suitable for population invasion. We focused on the siderophore pyoverdine produced by the human pathogen <jats:italic>Pseudomonas aeruginosa</jats:italic> MPAO1 and manipulated its uptake by deleting and/or overexpressing the pyoverdine primary (FpvA) and secondary (FpvB) receptors. We found that receptor synthesis feeds back on pyoverdine production and uptake rates, which led to strains with altered pyoverdine-associated costs and benefits. Moreover, we found that the receptor FpvB was advantageous under iron-limited conditions but revealed hidden costs in the presence of an antibiotic stressor (gentamicin). As a consequence, FpvB mutants became the fittest strain under gentamicin exposure, displacing the wildtype in liquid cultures, and in biofilms and during infections of the wax moth larvae <jats:italic>Galleria mellonella</jats:italic>, which both represent structured e
Kim J, Darlington A, Salvador M, et al., 2020, Trade-offs between gene expression, growth and phenotypic diversity in microbial populations, CURRENT OPINION IN BIOTECHNOLOGY, Vol: 62, Pages: 29-37, ISSN: 0958-1669
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- Citations: 38
Lastiri-Pancardo G, Mercado-Hernandez JS, Kim J, et al., 2019, A quantitative method for proteome reallocation using minimal regulatory interventions
<jats:title>Abstract</jats:title><jats:p>Engineering resource allocation in biological systems for synthetic biology applications is an ongoing challenge. Wild type organisms allocate abundant cellular resources for ensuring survival in changing environments, reducing the productivity of engineered functions. Here we present a novel approach for engineering the resource allocation of <jats:italic>Escherichia coli</jats:italic> by rationally modifying the transcriptional regulatory network of the bacterium. Our method (ReProMin) identifies the minimal set of genetic interventions that maximise the savings in cell resources that would normally be used to express non-essential genes. To this end we categorize Transcription Factors (TFs) according to the essentiality of the genes they regulate and we use available proteomic data to rank them based on its proteomic balance, defined as the net proteomic charge they release. Using a combinatorial approach, we design the removal of TFs that maximise the release of the proteomic charge and we validate the model predictions experimentally. Expression profiling of the resulting strain shows that our designed regulatory interventions are highly specific. We show that our resulting engineered strain containing only three mutations, theoretically releasing 0.5% of their proteome, has higher proteome budget and show increased production yield of a molecule of interest obtained from a recombinant metabolic pathway. This approach shows that combining whole-cell proteomic and regulatory data is an effective way of optimizing strains in a predictable way using conventional molecular methods.</jats:p><jats:sec><jats:title>Importance</jats:title><jats:p>Biological regulatory mechanisms are complex and occur in hierarchical layers such as transcription, translation and post-translational mechanisms. We foresee the use of regulatory mechanism as a control layer that will aid in t
Salvador M, Abdulmutalib U, Gonzalez J, et al., 2019, Microbial Genes for a Circular and Sustainable Bio-PET Economy, GENES, Vol: 10, ISSN: 2073-4425
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- Citations: 68
Salvador M, Abdulmutalib U, Gonzalez J, et al., 2019, Genes for a Circular and Sustainable Bio-PET Economy
<jats:p>Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as becoming a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decrease the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in the degradation of the polymer and the metabolism of the monomers and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.</jats:p>
Darlington APS, Kim J, Jimenez JI, et al., 2018, Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations, ACS SYNTHETIC BIOLOGY, Vol: 7, Pages: 2485-2496, ISSN: 2161-5063
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- Citations: 11
Darlington APS, Kim J, Jimenez JI, et al., 2018, Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes, NATURE COMMUNICATIONS, Vol: 9
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- Citations: 76
Darlington APS, Kim J, Jiménez JI, et al., 2018, Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations
<jats:title>Abstract</jats:title><jats:p>The use of orthogonal ribosomes in combination with dynamic resource allocation controllers is a promising approach for relieving the negative effects of cellular resource limitations on the modularity of synthetic gene circuits. Here, we develop a detailed mechanistic model of gene expression and resource allocation, which when simplified to a tractable level of complexity, allows the rational design of translational resource allocation controllers. Analysis of this model reveals a fundamental design trade-off; that reducing coupling acts to decrease gene expression. Through a sensitivity analysis of the experimentally tuneable controller parameters, we identify how each controller design parameter affects the overall closed-loop behaviour of the system, leading to a detailed set of design guidelines for optimally managing this trade-off. Based on our designs, we evaluated a number of alternative potential experimental implementations of the proposed system using commonly available biological components. Finally, we show that the controller is capable of dynamically allocating ribosomes as needed to restore modularity in a number of more complex synthetic circuits, such as the repressilator, and activation cascades composed of multiple interacting modules.</jats:p>
Cavaliere M, Feng S, Soyer OS, et al., 2017, Cooperation in microbial communities and their biotechnological applications, ENVIRONMENTAL MICROBIOLOGY, Vol: 19, Pages: 2949-2963, ISSN: 1462-2912
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- Citations: 90
Qian Y, Huang H-H, Jimenez JI, et al., 2017, Resource Competition Shapes the Response of Genetic Circuits, ACS SYNTHETIC BIOLOGY, Vol: 6, Pages: 1263-1272, ISSN: 2161-5063
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- Citations: 137
Darlington APS, Kim J, Jiménez JI, et al., 2017, Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes
<jats:title>Abstract</jats:title><jats:p>Introduction of synthetic circuits into host microbes creates competition between circuit and host genes for shared cellular resources, such as RNA polymerases and ribosomes. This can lead to the emergence of unwanted coupling between the expression of different genes, complicating circuit design and potentially leading to circuit failure. Here we demonstrate the ability of orthogonal ribosomes to alleviate the effects of this resource competition. We partition the ribosome pool by expressing an engineered 16S RNA with altered specificity, and use this division of specificity to build simple resource allocators which reduce the level of ribosome-mediated gene coupling. We then design and implement a dynamic resource allocation controller, which acts to increase orthogonal ribosome production as the demand for translational resources by a synthetic circuit increases. Our results highlight the potential of dynamic translational resource allocation as a means of minimising the impact of cellular limitations on the function of synthetic circuitry.</jats:p>
Jimenez JI, 2017, Shedding light on the black box models of the cell, MICROBIAL BIOTECHNOLOGY, Vol: 10, Pages: 43-45, ISSN: 1751-7915
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- Citations: 2
Avendano R, Chaves N, Fuentes P, et al., 2016, Production of selenium nanoparticles in <i>Pseudomonas putida</i> KT2440, SCIENTIFIC REPORTS, Vol: 6, ISSN: 2045-2322
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- Citations: 78
Xulvi-Brunet R, Campbell GW, Rajamani S, et al., 2016, Computational analysis of fitness landscapes and evolutionary networks from <i>in vitro</i> evolution experiments, METHODS, Vol: 106, Pages: 86-96, ISSN: 1046-2023
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- Citations: 8
Kim J, Salvador M, Saunders E, et al., 2016, Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis, SYNTHETIC BIOLOGY-BOOK, Vol: 60, Pages: 303-313, ISSN: 0071-1365
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- Citations: 30
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