Construction of synthetic regulatory networks in yeast

Yeast species such as Saccharomyces cerevisiae have been exploited by humans for millennia and so it is therefore unsurprising that they are attractive cells to re-engineer for industrial use. Despite many beneficial traits yeast has for synthetic biology, it currently lags behind Escherichia coli in the number of synthetic networks that have been described. While the eukaryotic nature of yeast means that its regulation is not as simple to predict as it is for E. coli, once initial considerations have been made yeast is pleasingly tractable. In this review we provide a loose guide for constructing and implementing synthetic regulatory networks in S. cerevisiae using examples from previous research to highlight available resources, specific considerations and potential future advances. © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved

The Effects of Chemical Interactions and Culture History on the Colonization of Structured Habitats by Competing Bacterial Populations: Data Set

We explored the colonization of a patchy ecosystem by two neutrally labeled, but otherwise isogenic, strains of Escherichia coli. One-dimensional arrays of habitat patches linked by connectors were inoculated at opposite ends by two fluorescently-labeled strains, and the colonization was studied by time-lapse microscopy. We focussed on the degree of reproducibility of the resulting colonization patterns and on the interactions between the two populations during the colonization process

Sensitivity of phytoplankton, zooplankton and macroinvertebrates to hydrogen peroxide treatments of cyanobacterial blooms

Addition of hydrogen peroxide (H2O2) is a promising method to acutely suppress cyanobacterial blooms in lakes. However, a reliable H2O2 risk assessment to identify potential effects on non-target species is currently hampered by a lack of appropriate ecotoxicity data. The aim of the present study was therefore to quantify the responses of a wide diversity of freshwater phytoplankton, zooplankton and macroinvertebrates to H2O2 treatments of cyanobacterial blooms. To this end, we applied a multifaceted approach. First, we investigated the 24-h toxicity of H2O2 to three cyanobacteria (Planktothrix agardhii, Microcystis aeruginosa, Anabaena sp.) and 23 non-target species (six green algae, eight zooplankton and nine macroinvertebrate taxa), using EC50 values based on photosynthetic yield for phytoplankton and LC50 values based on mortality for the other organisms. The most sensitive species included all three cyanobacterial taxa, but also the rotifer Brachionus calyciflores and the cladocerans Ceriodaphnia dubia and Daphnia pulex. Next, the EC50 and LC50 values obtained from the laboratory toxicity tests were used to construct a species sensitivity distribution (SSD) for H2O2. Finally, the species predicted to be at risk by the SSD were compared with the responses of phytoplankton, zooplankton and macroinvertebrates to two whole-lake treatments with H2O2. The predictions of the laboratory-based SSD matched well with the responses of the different taxa to H2O2 in the lake. The first lake treatment, with a relatively low H2O2 concentration and short residence time, successfully suppressed cyanobacteria without major effects on non-target species. The second lake treatment had a higher H2O2 concentration with a longer residence time, which resulted in partial suppression of cyanobacteria, but also in a major collapse of rotifers and decreased abundance of small cladocerans. Our results thus revealed a trade-off between the successful suppression of cyanobacteria at the expense of adverse effects on part of the zooplankton community. This delicate balance strongly depends on the applied H2O2 dosage and may affect the decision whether to treat a lake or not.</p

Shifts in phytoplankton and zooplankton communities in three cyanobacteria-dominated lakes after treatment with hydrogen peroxide

Cyanobacteria can reach high densities in eutrophic lakes, which may cause problems due to their potential toxin production. Several methods are in use to prevent, control or mitigate harmful cyanobacterial blooms. Treatment of blooms with low concentrations of hydrogen peroxide (H2O2) is a promising emergency method. However, effects of H2O2 on cyanobacteria, eukaryotic phytoplankton and zooplankton have mainly been studied in controlled cultures and mesocosm experiments, while much less is known about the effectiveness and potential side effects of H2O2 treatments on entire lake ecosystems. In this study, we report on three different lakes in the Netherlands that were treated with average H2O2 concentrations ranging from 2 to 5 mg L−1 to suppress cyanobacterial blooms. Effects on phytoplankton and zooplankton communities, on cyanotoxin concentrations, and on nutrient availability in the lakes were assessed. After every H2O2 treatment, cyanobacteria drastically declined, sometimes by more than 99%, although blooms of Dolichospermum sp., Aphanizomenon sp., and Planktothrix rubescens were more strongly suppressed than a Planktothrix agardhii bloom. Eukaryotic phytoplankton were not significantly affected by the H2O2 additions and had an initial advantage over cyanobacteria after the treatment, when ample nutrients and light were available. In all three lakes, a new cyanobacterial bloom developed within several weeks after the first H2O2 treatment, and in two lakes a second H2O2 treatment was therefore applied to again suppress the cyanobacterial population. Rotifers strongly declined after most H2O2 treatments except when the H2O2 concentration was ≤ 2 mg L−1, whereas cladocerans were only mildly affected and copepods were least impacted by the added H2O2. In response to the treatments, the cyanotoxins microcystins and anabaenopeptins were released from the cells into the water column, but disappeared after a few days. We conclude that lake treatments with low concentrations of H2O2 can be a successful tool to suppress harmful cyanobacterial blooms, but may negatively affect some of the zooplankton taxa in lakes. We advise pre-tests prior to the treatment of lakes to define optimal treatment concentrations that kill the majority of the cyanobacteria and to minimize potential side effects on non-target organisms. In some cases, the pre-tests may discourage treatment of the lake.</p

Shifts in phytoplankton and zooplankton communities in three cyanobacteria-dominated lakes after treatment with hydrogen peroxide

Cyanobacteria can reach high densities in eutrophic lakes, which may cause problems due to their potential toxin production. Several methods are in use to prevent, control or mitigate harmful cyanobacterial blooms. Treatment of blooms with low concentrations of hydrogen peroxide (H2O2) is a promising emergency method. However, effects of H2O2 on cyanobacteria, eukaryotic phytoplankton and zooplankton have mainly been studied in controlled cultures and mesocosm experiments, while much less is known about the effectiveness and potential side effects of H2O2 treatments on entire lake ecosystems. In this study, we report on three different lakes in the Netherlands that were treated with average H2O2 concentrations ranging from 2 to 5 mg L−1 to suppress cyanobacterial blooms. Effects on phytoplankton and zooplankton communities, on cyanotoxin concentrations, and on nutrient availability in the lakes were assessed. After every H2O2 treatment, cyanobacteria drastically declined, sometimes by more than 99%, although blooms of Dolichospermum sp., Aphanizomenon sp., and Planktothrix rubescens were more strongly suppressed than a Planktothrix agardhii bloom. Eukaryotic phytoplankton were not significantly affected by the H2O2 additions and had an initial advantage over cyanobacteria after the treatment, when ample nutrients and light were available. In all three lakes, a new cyanobacterial bloom developed within several weeks after the first H2O2 treatment, and in two lakes a second H2O2 treatment was therefore applied to again suppress the cyanobacterial population. Rotifers strongly declined after most H2O2 treatments except when the H2O2 concentration was ≤ 2 mg L−1, whereas cladocerans were only mildly affected and copepods were least impacted by the added H2O2. In response to the treatments, the cyanotoxins microcystins and anabaenopeptins were released from the cells into the water column, but disappeared after a few days. We conclude that lake treatments with low concentrations of H2O2 can be a successful tool to suppress harmful cyanobacterial blooms, but may negatively affect some of the zooplankton taxa in lakes. We advise pre-tests prior to the treatment of lakes to define optimal treatment concentrations that kill the majority of the cyanobacteria and to minimize potential side effects on non-target organisms. In some cases, the pre-tests may discourage treatment of the lake.</p

Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions

Expanding the regulatory repertoire available for synthetic genetic circuits in S. cerevisiae.

Complexity is arguably the biggest challenge to the field of synthetic biology today. As synthetic constructs include more and more parts, their performance becomes less predictable and more costly to host cells. In this thesis, we work towards the expansion of the regulatory repertoire available for S. cerevisiae with the aim of reducing the complexity of synthetic gene circuits and thus improving their performance. Three projects contribute to achieving this goal. First, we note that no tool exists for yeast similar to the bacterial RBS Calculator that enables accurate tuning of expression levels. We address this by designing a system for tuning translation efficiency based on predictable hairpin structures placed in mRNA 5’UTRs. We characterise the relationship between folding strength and expression output and show that this facilitates predictable expression level tuning. We implement this system as a method for rapid library generation and characterise it with regards to both context and predictability. Next, we implement transcriptional interference (TI) as a tool to augment existing regulatory interactions that may not possess sufficient regulatory power to implement the desired function. We demonstrate that TI performs as expected at the mRNA level, but observe that the imple- mentation interferes with translational output. We test a variety of solutions relying on different molecular mechanisms within the host and conclude with a system for functionalising the RNA product produced. In the third project, we implement a system for simplifying circuit designs by combining activation and repression functionality into a single transcription factor. This system is based on TAL-effectors fused to an activation domain that can be targeted to an upstream region of a promoter for activation and a downstream region for repression. In a systematic series of characterisation experiments we show the creation of a TAL-effector promoter pair that exhibits the desired functionality.Open Acces

The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations

Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the colonization of a structured ecosystem by two neutrally labeled strains of Escherichia coli. Using time-lapse microscopy we studied the colonization of one-dimensional arrays of habitat patches linked by connectors, which were invaded by the two E. coli strains from opposite sides.; The two strains colonize a habitat from opposite sides by a series of traveling waves followed by an expansion front. When population waves collide, they branch into a continuing traveling wave, a reflected wave and a stationary population. When the two strains invade the landscape from opposite sides, they remain segregated in space and often one population will displace the other from most of the habitat. However, when the strains are co-cultured before entering the habitats, they colonize the habitat together and do not separate spatially. Using physically separated, but diffusionally coupled, habitats we show that colonization waves and expansion fronts interact trough diffusible molecules, and not by direct competition for space. Furthermore, we found that colonization outcome is influenced by a culture's history, as the culture with the longest doubling time in bulk conditions tends to take over the largest fraction of the habitat. Finally, we observed that population distributions in parallel habitats located on the same device and inoculated with cells from the same overnight culture are significantly more similar to each other than to patterns in identical habitats located on different devices inoculated with cells from different overnight cultures, even tough all cultures were started from the same -80°C frozen stock.; We found that the colonization of spatially structure habitats by two interacting populations can lead to the formation of complex, but reproducible, spatiotemporal patterns. Furthermore, we showed that chemical interactions between two populations cause them to remain spatially segregated while they compete for habitat space. Finally, we observed that growth properties in bulk conditions correlate with the outcome of habitat colonization. Together, our data show the crucial roles of chemical interactions between populations and a culture's history in determining the outcome of habitat colonization

Characterisation of <i>PFY1</i>p against 5 other yeast promoters.

<p>Fluorescence output of chromosomal single-copy <i>yEGFP</i> under the control of <i>ADH1</i>p, <i>BIO2</i>p, <i>CHO1</i>p, <i>CIT2</i>p, <i>CYC1</i>p and <i>PFY1</i>p as determined by flow cytometry in triplicate. Fluorescence is displayed in arbitrary fluorescence units (AFU) and represents the mean average of the geometric mean values of three replicate cultures. Media types are YPD, and SC media with 2% glucose (Glu), galactose (Gal), glycerol (Gly) or glucose and ethanol (GE) as added carbon sources. Coefficient of variation (CV) is calculated using geometric mean values from each replicate under each media condition at each time point.</p