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Metabolic engineering of yeast is an attractive way to produce advanced biofuels. However, engineering of yeast by introducing heterologous proteins and pathways can reduce growth rates and impact productivity. Towards optimizing yeast strains, sensor-regulators can assist the optimal usage of cellular resources, where protein expression can be regulated by the concentration of important metabolites. In this thesis, synthetic promoters were engineered and heterologous transcriptional repressors were expressed in order to create dynamic controllers in yeast. First, fatty acids/fatty acyl-CoA sensor-regulators were made as they are key intermediates in the production of fatty acid derived biofuels, which are suitable for direct use in current transportation infrastructure. This enables fatty acid dependant control of fatty acid derivative producing proteins. Second, AND-gate dynamic controllers that combine inducible promoter function, which enables cells to quickly accumulate biomass before triggering the production of biofuel producing proteins, and fatty acid sensing-regulation were constructed. Third, xylose sensor-regulators were created, where xylose is a major sugar component in the affordable lignocellulose biomass carbon source. This allows regulation of xylose utilizing proteins based on the amount of xylose sugars detected. The function and performance of these synthetic promoters to dynamically control yEGFP reporter protein were demonstrated. DOCTOR OF PHILOSOPHY (SCBE)

SummaryWe present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable.

Synthetic biologists construct biological components and systems to look into biological phenomena and drive a myriad of practical applications that aim to tackle current global challenges in energy, healthcare and the environment. While most tools have been established in bacteria, particularly Escherichia coli, recent years have seen parallel developments in the model yeast strain Saccharomyces cerevisiae, one of the most well-understood eukaryotic biological system. Here, we outline the latest advances in yeast synthetic biology tools based on a framework of abstraction hierarchies of parts, circuits and genomes. In brief, the creation and characterization of biological parts are explored at the transcriptional, translational and post-translational levels. Using characterized parts as building block units, the designing of functional circuits is elaborated with examples. In addition, the status and potential applications of synthetic genomes as a genome level platform for biological system construction are also discussed. In addition to the development of a toolkit, we describe how those tools have been applied in the areas of drug production and screening, study of disease mechanisms, pollutant sensing and bioremediation. Finally, we provide a future outlook of yeast as a workhorse of eukaryotic genetics and a chosen chassis in this field.

Lignocellulosic biomass is a sustainable and abundant starting material for biofuel production. However, lignocellulosic hydrolysates contain not only glucose, but also other sugars including xylose which cannot be metabolized by the industrial workhorse Saccharomyces cerevisiae. Hence, engineering of xylose assimilating S. cerevisiae has been much studied, including strain optimization strategies. In this work, we constructed genetically encoded xylose biosensors that can control protein expression upon detection of xylose sugars. These were constructed with the constitutive expression of heterologous XylR repressors, which function as protein sensors, and cloning of synthetic promoters with XylR operator sites. Three XylR variants and the corresponding synthetic promoters were used: XylR from Tetragenococcus halophile, Clostridium difficile, and Lactobacillus pentosus. To optimize the biosensor, two promoters with different strengths were used to express the XylR proteins. The ability of XylR to repress yEGFP expression from the synthetic promoters was demonstrated. Furthermore, xylose sugars added exogenously to the cells were shown to regulate gene expression. We envision that the xylose biosensors can be used as a tool to engineer and optimize yeast that efficiently utilizes xylose as carbon source for growth and biofuel production.

Efficient production of biochemicals using engineered microbes as whole-cell biocatalysts requires robust cell viability. Robust viability leads to high productivity and improved bioprocesses by allowing repeated cell recycling. However, cell viability is negatively affected by a plethora of stresses, namely chemical toxicity and metabolic imbalances, primarily resulting from bio-synthesis pathways. Chemical toxicity is caused by substrates, intermediates, products, and/or by-products, and these compounds often interfere with important metabolic processes and damage cellular infrastructures such as cell membrane, leading to poor cell viability. Further, stresses on engineered cells are accentuated by metabolic imbalances, which are generated by heavy metabolic resource consumption due to enzyme overexpression, redistribution of metabolic fluxes, and impaired intracellular redox state by co-factor imbalance. To address these challenges, herein, we discuss a range of key microbial engineering strategies, substantiated by recent advances, to improve cell viability for commercially sustainable production of biochemicals from renewable resources.

Fatty acid derivatives have ideal properties for use as drop-in biofuels. An effective strategy in engineering microbial cells to maximize productivity and yield involves dynamic control of protein production in response to concentrations of key intermediates. In Saccharomyces cerevisiae, the activities of the native transcription factors responsive to fatty acids are repressed in the presence of a glucose carbon source. In order to develop a modular fatty acid regulation system in S. cerevisiae, we constructed fatty acid/fatty acyl-CoA biosensors in S. cerevisiae using bacterial FadR transcriptional repressors and yeast synthetic promoters containing DNA-binding operators. We demonstrated the functionality of FadR repressors in S. cerevisiae, and tuned the sensing system by varying the promoter strength upstream to the FadR-coding sequence by varying the number of operator sites in the synthetic promoter and by using FadR from two bacterial sources (Escherichia coli and Vibrio cholerae) with different ligand sensitivities. We envision that our fatty acid/fatty acyl-CoA biosensors can be used for regulation of protein expression based on the availability of fatty acid intermediates, which will assist in balancing of cellular metabolism during fatty acid derivatives production in yeast.

Expression of heterologous proteins in metabolic engineering endeavors can be detrimental to host cells due to increased usage of cellular resources. Dynamic controls, where protein expression can be triggered on-demand, are effective for the engineering and optimization of bio-catalysts towards robust cell growth and enhanced biochemical productivity. Here, we describe the development and characterization of AND-gate dynamic controllers in Saccharomyces cerevisiae which combine two dynamic control strategies, inducible promoters and sensing-regulation. These dynamic controllers were constructed based on synthetic hybrid promoters. Promoter enhancer sequences were fused to a synthetic GAL1 core promoter containing DNA binding sites for the binding of a repressor that reduced DNA affinity upon interaction with key intermediates in a biochemical pathway. As fatty acids are key intermediates for production of fatty alcohols, fatty acid esters, alkenes, and alkanes, which are advanced biofuels, we used the fatty acid responsive FadR repressor and its operator sequence to demonstrate the functionality of the dynamic controllers. We established that the synthetic GAL1 core promoter can be used as a modular promoter part for constructing synthetic hybrid promoters and conferring fatty acid inducibility. We further showed the performance of the AND-gate dynamic controllers, where two inputs (fatty acid and copper presence/phosphate starvation) were required to switch the AND-gate ON. This work provides a convenient platform for constructing AND-gate dynamic controllers, that is, promoters that combine inducible functionality with regulation of protein expression levels upon detection of key intermediates towards the engineering and optimization of bio-catalytic yeast cells.

Stem cell therapies offer enormous hope for treating many tragic diseases and tissue defects. In particular, mesenchymal stem/multipotent stromal cells (MSCs) are capable of differentiating into multiple types of connective tissues (i.e., bone, cartilage, and even muscle and neuron) and have proangiogeneic and immunomodulatory effects. MSCs have potential utility for treating a variety of diseases and disorders, including graft versus host disease, problems related to organ transplantation, cardiovascular disease, brain and spinal cord injury, lung, liver, and kidney diseases, and skeletal injuries. This chapter summarizes the current status of therapeutic applications of MSCs. It begins by introducing the basics of MSCs and then focuses on their therapeutic potential, including mechanism of action, delivery routes, MSC homing, the current status of clinical trials, and potential challenges and safety issues. Finally, the chapter describes chemical approaches developed in the authors’ laboratory to promote homing and engraftment of systemically infused MSCs within specific tissues.

Background Biodiesel is a mixture of fatty acid short-chain alkyl esters of different fatty acid carbon chain lengths. However, while fatty acid methyl or ethyl esters are useful biodiesel produced commercially, fatty acid esters with branched-chain alcohol moieties have superior fuel properties. Crucially, this includes improved cold flow characteristics, as one of the major problems associated with biodiesel use is poor low-temperature flow properties. Hence, microbial production as a renewable, nontoxic and scalable method to produce fatty acid esters with branched-chain alcohol moieties from biomass is critical. Results We engineered Saccharomyces cerevisiae to produce fatty acid short- and branched-chain alkyl esters, including ethyl, isobutyl, isoamyl and active amyl esters using endogenously synthesized fatty acids and alcohols. Two wax ester synthase genes (ws2 and Maqu_0168 from Marinobacter sp.) were cloned and expressed. Both enzymes were found to catalyze the formation of fatty acid esters, with different alcohol preferences. To boost the ability of S. cerevisiae to produce the aforementioned esters, negative regulators of the INO1 gene in phospholipid metabolism, Rpd3 and Opi1, were deleted to increase flux towards fatty acyl-CoAs. In addition, five isobutanol pathway enzymes (Ilv2, Ilv5, Ilv3, Aro10, and Adh7) targeted into the mitochondria were overexpressed to enhance production of alcohol precursors. By combining these engineering strategies with high-cell-density fermentation, over 230 mg/L fatty acid short- and branched-chain alkyl esters were produced, which is the highest titer reported in yeast to date. Conclusions In this work, we engineered the metabolism of S. cerevisiae to produce biodiesels in the form of fatty acid short- and branched-chain alkyl esters, including ethyl, isobutyl, isoamyl and active amyl esters. To our knowledge, this is the first report of the production of fatty acid isobutyl and active amyl esters in S. cerevisiae. Our findings will be useful for engineering S. cerevisiae strains toward high-level and sustainable biodiesel production. Electronic supplementary material The online version of this article (doi:10.1186/s13068-015-0361-5) contains supplementary material, which is available to authorized users.