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Salty taste has evolved to maintain electrolyte homeostasis, serving as a detector for salt containing food. In rodents, salty taste involves at least two transduction mechanisms. One is sensitive to the drug amiloride and specific for Na+, involving epithelial sodium channel (ENaC). A second rodent transduction pathway, which is triggered by various cations, is amiloride insensitive and not almost understood to date. Studies in primates showed amiloride-sensitive as well as amiloride-insensitive gustatory responses to NaCl, implying a role of both salt taste transduction pathways in humans. However, sensory studies in humans point to largely amiloride-insensitive sodium taste perception. An involvement of ENaC in human sodium taste perception was not shown, so far. In this study, ENaC subunit protein and mRNA could be localized to human taste bud cells (TBC). Thus, basolateral αβγ-ENaC ion channels are likely in TBC of circumvallate papillae, possibly mediating basolateral sodium entry. Similarly, basolateral βγ-ENaC might play a role in fungiform TBC. Strikingly, δ-ENaC subunit was confined to taste bud pores of both papillae, likely mediating gustatory sodium entry in TBC, either apical or paracellular via tight junctions. However, regional separation of δ-ENaC and βγ-ENaC in fungiform and circumvallate TBC indicate the presence of unknown interaction partner necessary to assemble into functional ion channels. However, screening of a macaque taste tissue cDNA library did neither reveal polypeptides assembling into a functional cation channel by interaction with δ-ENaC or βγ-ENaC nor ENaC independent salt taste receptor candidates. Thus, ENaC subunits are likely involved in human taste transduction, while exact composition and identity of an amiloride (in)sensitive salt taste receptors remain unclear. Localization of δ-ENaC in human taste pores strongly suggests a role in human taste transduction. In contrast, δ-ENaC is classified as pseudogene Scnn1d in mouse. However, no experimental detected sequences are annotated, while evidences for parts of Scnn1d derived mRNAs exist. In order to elucidate if Scnn1d is possibly involved in rodent salt taste perception, Scnn1d was evaluated in this study to clarify if Scnn1d is a gene or a transcribed pseudogene in mice. Comparative mapping of human SCNN1D to mouse chromosome 4 revealed complete Scnn1d sequence as well as its pseudogenization by Mus specific endogenous retroviruses. Moreover, tissue specific transcription of unitary Scnn1d pseudogene was found in mouse vallate papillae, kidney and testis and led to identification of nine Scnn1d transcripts. In vitro translation experiments showed that Scnn1d transcripts are coding competent for short polypeptides, possibly present in vivo. However, no sodium channel like function or sodium channel modulating activity was evident for Scnn1d transcripts and/or derived polypeptides. Thus, an involvement of mouse δ-ENaC in sodium taste transduction is unlikely and points to species specific differences in salt taste transduction mechanisms.
As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O2 affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.
The link between emotions and motor function has been known for decades but is still not clarified. The Adaptive Force (AF) describes the neuromuscular capability to adapt to increasing forces and was suggested to be especially vulnerable to interfering inputs. This study investigated the influence of pleasant an unpleasant food imagery on the manually assessed AF of elbow and hip flexors objectified by a handheld device in 12 healthy women. The maximal isometric AF was significantly reduced during unpleasant vs. pleasant imagery and baseline (p < 0.001, dz = 0.98–1.61). During unpleasant imagery, muscle lengthening started at 59.00 ± 22.50% of maximal AF, in contrast to baseline and pleasant imagery, during which the isometric position could be maintained mostly during the entire force increase up to ~97.90 ± 5.00% of maximal AF. Healthy participants showed an immediately impaired holding function triggered by unpleasant imagery, presumably related to negative emotions. Hence, AF seems to be suitable to test instantaneously the effect of emotions on motor function. Since musculoskeletal complaints can result from muscular instability, the findings provide insights into the understanding of the causal chain of linked musculoskeletal pain and mental stress. A case example (current stress vs. positive imagery) suggests that the approach presented in this study might have future implications for psychomotor diagnostics and therapeutics.
The link between emotions and motor function has been known for decades but is still not clarified. The Adaptive Force (AF) describes the neuromuscular capability to adapt to increasing forces and was suggested to be especially vulnerable to interfering inputs. This study investigated the influence of pleasant an unpleasant food imagery on the manually assessed AF of elbow and hip flexors objectified by a handheld device in 12 healthy women. The maximal isometric AF was significantly reduced during unpleasant vs. pleasant imagery and baseline (p < 0.001, dz = 0.98–1.61). During unpleasant imagery, muscle lengthening started at 59.00 ± 22.50% of maximal AF, in contrast to baseline and pleasant imagery, during which the isometric position could be maintained mostly during the entire force increase up to ~97.90 ± 5.00% of maximal AF. Healthy participants showed an immediately impaired holding function triggered by unpleasant imagery, presumably related to negative emotions. Hence, AF seems to be suitable to test instantaneously the effect of emotions on motor function. Since musculoskeletal complaints can result from muscular instability, the findings provide insights into the understanding of the causal chain of linked musculoskeletal pain and mental stress. A case example (current stress vs. positive imagery) suggests that the approach presented in this study might have future implications for psychomotor diagnostics and therapeutics.
Lying is an everyday moral phenomenon about which philosophers have written a lot. Not only the moral status of lying has been intensively discussed but also what it means to lie in the first place. Perhaps the most important criterion for an adequate definition of lying is that it fits with people’s understanding and use of this concept. In this light, it comes as a surprise that researchers only recently started to empirically investigate the folk concept of lying. In this paper, we describe three experimental studies which address the following questions: Does a statement need to be objectively false in order to constitute lying? Does lying necessarily include the intention to deceive? Can one lie by omitting relevant facts?
Humans are frequently exposed to a variety of endocrine disrupting chemicals (EDCs), which can cause harmful effects, e.g. disturbance of growth, development and reproduction, and cancer (UBA, 2016). EDCs are often components of synthetically manufactured products. Materials made of plastics, building materials, electronic items, textiles or cosmetic products can be particularly contaminated (Ain et al., 2021). One group of EDCs that has gained increased interest in recent years is phthalates. They are used as plasticizers in plastic materials to which people are daily exposed to. Phthalate plasticizers exert their harmful effects among others via activation of the estrogen receptor α (ERα), the estrogen receptor β (ERβ) and via inhibition of the androgen receptor (AR). Some phthalates have already been classified by the EU as Cancerogenic-, Mutagenic-, Reprotoxic- (CMR) substances and their use in industry has been restricted. After oral ingestion, phthalates are metabolized and are finally excreted with the urine. Numerous toxicological studies exist on phthalates, but mainly with the parent substances, not with their primary and secondary metabolites. In the course of the restriction of phthalates by the EU, the phthalate-free plasticizer di-isononylcyclohexane-1,2-dicarboxylate (DINCH®), was introduced to the market. So far, almost no toxicologically relevant properties have been identified for DINCH®. However, the effects of DINCH® have only been studied in animal experiments and, as with phthalates, almost exclusively with the parent substance. However, toxic effects of a particular compound may be induced by its metabolites and not by the parent compound itself. Therefore, potential endocrine effects of 15 phthalates, 19 phthalate metabolites, DINCH®, and five of its metabolites were investigated using reporter gene assays on the ERα, ERβ, and the AR. In addition, studies of the influence of some selected plasticizers on peroxisome proliferator-activated receptor α (PPARα) and peroxisome proliferator-activated receptor γ (PPARγ) activity were performed. Furthermore, a H295R steroidogenesis assay was performed to determine the influence of DINCH® and its metabolites on estradiol or testosterone synthesis. Analysis of the experiments shows that the phthalates either stimulated or inhibited ERα and ERβ activity and inhibited AR activity, whereas the phthalate metabolites did not affect the activity of these human hormone receptors. In contrast, metabolites of di-(2-ethylhexyl) phthalate (DEHP) stimulated transactivation of the human PPARα and PPARγ in analogous reporter gene assays, although DEHP itself did not activate these nuclear receptors. Therefore, primary and secondary phthalate metabolites appear to exert different effects at the molecular level compared to the parent compounds. Similarly, the results showed that the phthalate-free plasticizer DINCH® itself did not affect the activity of ERα, ERβ, AR, PPARα and PPARγ, while the DINCH® metabolites were shown to activate all these receptors. In the case of AR, DINCH® metabolites mainly enhanced AR activity stimulated by dihydrotestosterone (DHT). In the H295R steroidogenesis assay, neither DINCH® nor any of its metabolites affected estradiol or testosterone synthesis. Primary and secondary metabolites of DINCH® thus exert different effects at the molecular level than DINCH® itself. However, all these in vitro effects of DINCH® metabolites were observed only at high concentrations, which were about three orders of magnitude higher than the reported DINCH® metabolite concentrations in human urine. Therefore, the in vitro data does not support the assumption that DINCH® or any of the metabolites studied could have significant endocrine effects in vivo at relevant exposure levels in humans. Following the demonstration of direct and indirect endocrine effects of the studied plasticizers, a new effect-based in vitro 3D screening tool for toxicity assays of non-genotoxic carcinogens was developed using estrogen receptor-negative (ER-) MCF10-A cells and estrogen receptor-positive (ER+) MCF-12A cells. This arose from the background that breast cancer is the most common cancer occurring in women and estrogenic substances, such as phthalates, can probably influence the disease. The human mammary epithelial cell lines MCF-10A and MCF-12A form well-differentiated acini-like structures when cultured in three-dimensional Matrigel culture for a period of 20 days. The model should make it possible to detect substance effects on cell differentiation and growth, on mammary cell acini, and to differentiate between estrogenic and non-estrogenic effects at the same time. In the present study, both cell lines were tested for their suitability as an effect-based in vitro assay system for non-genotoxic carcinogens. An Automated Acinus Detection And Morphological Evaluation (ADAME) software solution has been developed for automatic acquisition of acinus images and determination of morphological parameters such as acinus size, lumen size, and acinus roundness. Several test substances were tested for their ability to affect acinus formation and cellular differentiation. Human epithelial growth factor (EGF) stimulated acinus growth for both cell lines, while all trans retinoic acid (RA) inhibited acinar growth. The potent estrogen 17β-estradiol had no effect on acinus formation of MCF-10A cells but resulted in larger MCF-12A acini. Thus, the parallel use of both cell lines together with the developed high content screening and evaluation tool allows the rapid identification of the estrogenic and cancerogenic properties of a given test compound. The morphogenesis of the acini was only slightly affected by the test substances. On the one hand, this suggests a robust test system, on the other hand, it probably cannot detect low-potent estrogenic compounds such as phthalates or DINCH®. The advantage of the robustness of the system, however, may be that vast numbers of "positive" results with questionable biological relevance could be avoided, such as those observed in sensitive reporter gene assays.
Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present.
Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences.
Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.
Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present.
Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences.
Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.
BACKGROUND: The formation of a functionally-confluent endothelial cell (EC) monolayer affords proliferation of EC, which only happens in case of appropriate migratory activity. AIM OF THE STUDY: The migratory pathway of human umbilical endothelial cells (HUVEC) was investigated on different polymeric substrates. MATERIAL AND METHODS: Surface characterization of the polymers was performed by contact angle measurements and atomic force microscopy under wet conditions. 30,000 HUVEC per well were seeded on polytetrafluoroethylene (PTFE) (theta(adv) = 119 degrees +/- 2 degrees), on low-attachment plate LAP (theta(adv) = 28 degrees +/- 2 degrees) and on polystyrene based tissue culture plates (TCP, theta(adv) = 22 degrees +/- 1 degrees). HUVEC tracks (trajectories) were recorded by time lapse microscopy and the euclidean distance (straight line between starting and end point), the total distance and the velocities of HUVEC not leaving the vision field were determined. RESULTS: On PTFE, 42 HUVEC were in the vision field directly after seeding. The mean length of single migration steps (SML) was 6.1 +/- 5.2 mu m, the mean velocity (MV) 0.40 +/- 0.3 mu m.min(-1) and the complete length of the trajectory (LT) was 710 +/- 440 mu m. On TCP 82 HUVEC were in the vision field subsequent to seeding. The LT was 840 +/- 550 mu m, the SML 6.1 +/- 5.2 mu m and the MV 0.44 +/- 0.3 mu m.min(-1). The trajectories on LAP differed significantly in respect to SML (2.4 +/- 3.9 mu m, p <0.05), the MV (0.16 +/- 0.3 mu m.min(-1), p <0.05) and the LT (410 +/- 300 mu m, p <0.05), compared to PTFE and TCP. Solely on TCP a nearly confluent EC monolayer developed after three days. While on TCP diffuse signals of vinculin were found over the whole basal cell surface organizing the binding of the cells by focal adhesions, on PTFE vinculin was merely arranged at the cell rims, and on the hydrophilic material (LAP) no focal adhesions were found. CONCLUSION: The study revealed that the wettability of polymers affected not only the initial adherence but also the migration of EC, which is of importance for the proliferation and ultimately the endothelialization of polymer-based biomaterials.
Research in rodents has shown that dietary vitamin A reduces body fat by enhancing fat mobilisation and energy utilisation; however, their effects in growing dogs remain unclear. In the present study, we evaluated the development of body weight and body composition and compared observed energy intake with predicted energy intake in forty-nine puppies from two breeds (twenty-four Labrador Retriever (LAB) and twenty-five Miniature Schnauzer (MS)). A total of four different diets with increasing vitamin A content between 5.24 and 104.80 mu mol retinol (5000-100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy were fed from the age of 8 weeks up to 52 (MS) and 78 weeks (LAB). The daily energy intake was recorded throughout the experimental period. The body condition score was evaluated weekly using a seven-category system, and food allowances were adjusted to maintain optimal body condition. Body composition was assessed at the age of 26 and 52 weeks for both breeds and at the age of 78 weeks for the LAB breed only using dual-energy X-ray absorptiometry. The growth curves of the dogs followed a breed-specific pattern. However, data on energy intake showed considerable variability between the two breeds as well as when compared with predicted energy intake. In conclusion, the data show that energy intakes of puppies particularly during early growth are highly variable; however, the growth pattern and body composition of the LAB and MS breeds are not affected by the intake of vitamin A at levels up to 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal).
Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51%) despite the compromised luminescence due to surface quenching.
Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d ']bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51%) despite the compromised luminescence due to surface quenching.
The aim of this thesis is the design, expression and purification of human cytochrome c mutants and their characterization with regard to electrochemical and structural properties as well as with respect to the reaction with the superoxide radical and the selected proteins sulfite oxidase from human and fungi bilirubin oxidase. All three interaction partners are studied here for the first time with human cyt c and with mutant forms of cyt c. A further aim is the incorporation of the different cyt c forms in two bioelectronic systems: an electrochemical superoxide biosensor with an enhanced sensitivity and a protein multilayer assembly with and without bilirubin oxidase on electrodes. The first part of the thesis is dedicated to the design, expression and characterization of the mutants. A focus is here the electrochemical characterization of the protein in solution and immobilized on electrodes. Further the reaction of these mutants with superoxide was investigated and the possible reaction mechanisms are discussed. In the second part of the work an amperometric superoxide biosensor with selected human cytochrome c mutants was constructed and the performance of the sensor electrodes was studied. The human wild-type and four of the five mutant electrodes could be applied successfully for the detection of the superoxide radical. In the third part of the thesis the reaction of horse heart cyt c, the human wild-type and seven human cyt c mutants with the two proteins sulfite oxidase and bilirubin oxidase was studied electrochemically and the influence of the mutations on the electron transfer reactions was discussed. Finally protein multilayer electrodes with different cyt form including the mutant forms G77K and N70K which exhibit different reaction rates towards BOD were investigated and BOD together with the wild-type and engineered cyt c was embedded in the multilayer assembly. The relevant electron transfer steps and the kinetic behavior of the multilayer electrodes are investigated since the functionality of electroactive multilayer assemblies with incorporated redox proteins is often limited by the electron transfer abilities of the proteins within the multilayer. The formation via the layer-by-layer technique and the kinetic behavior of the mono and bi-protein multilayer system are studied by SPR and cyclic voltammetry. In conclusion this thesis shows that protein engineering is a helpful instrument to study protein reactions as well as electron transfer mechanisms of complex bioelectronic systems (such as bi-protein multilayers). Furthermore, the possibility to design tailored recognition elements for the construction of biosensors with an improved performance is demonstrated.
Increasing demand for food, healthcare, and transportation arising from the growing world population is accompanied by and driving global warming challenges due to the rise of the atmospheric CO2 concentration. Industrialization for human needs has been increasingly releasing CO2 into the atmosphere for the last century or more. In recent years, the possibility of recycling CO2 to stabilize the atmospheric CO2 concentration and combat rising temperatures has gained attention. Thus, using CO2 as the feedstock to address future world demands is the ultimate solution while controlling the rapid climate change. Valorizing CO2 to produce activated and stable one-carbon feedstocks like formate and methanol and further upgrading them to industrial microbial processes to replace unsustainable feedstocks would be crucial for a future biobased circular economy. However, not all microbes can grow on formate as a feedstock, and those microbes that can grow are not well established for industrial processes.
S. cerevisiae is one of the industrially well-established microbes, and it is a significant contributor to bioprocess industries. However, it cannot grow on formate as a sole carbon and energy source. Thus, engineering S. cerevisiae to grow on formate could potentially pave the way to sustainable biomass and value-added chemicals production.
The Reductive Glycine Pathway (RGP), designed as the aerobic twin of the anaerobic Reductive Acetyl-CoA pathway, is an efficient formate and CO2 assimilation pathway. The RGP comprises of the glycine synthesis module (Mis1p, Gcv1p, Gcv2p, Gcv3p, and Lpd1p), the glycine to serine conversion module (Shmtp), the pyruvate synthesis module (Cha1p), and the energy supply module (Fdh1p). The RGP requires formate and elevated CO2 levels to operate the glycine synthesis module. In this study, I established the RGP in the yeast system using growth-coupled selection strategies to achieve formate and CO2-dependent biomass formation in aerobic conditions.
Firstly, I constructed serine biosensor strains by disrupting the native serine and glycine biosynthesis routes in the prototrophic S288c and FL100 yeast strains and insulated serine, glycine, and one-carbon metabolism from the central metabolic network. These strains cannot grow on glucose as the sole carbon source but require the supply of serine or glycine to complement the engineered auxotrophies. Using growth as a readout, I employed these strains as selection hosts to establish the RGP. Initially, to achieve this, I engineered different serine-hydroxymethyltransferases in the genome of serine biosensor strains for efficient glycine to serine conversion. Then, I implemented the glycine synthesis module of the RGP in these strains for the glycine and serine synthesis from formate and CO2. I successfully conducted Adaptive Laboratory Evolution (ALE) using these strains, which yielded a strain capable of glycine and serine biosynthesis from formate and CO2. Significant growth improvements from 0.0041 h-1 to 0.03695 h-1 were observed during ALE. To validate glycine and serine synthesis, I conducted carbon tracing experiments with 13C formate and 13CO2, confirming that more than 90% of glycine and serine biosynthesis in the evolved strains occurs via the RGP. Interestingly, labeling data also revealed that 10-15% of alanine was labelled, indicating pyruvate synthesis from the formate-derived serine using native serine deaminase (Cha1p) activity. Thus, RGP contributes to a small pyruvate pool which is converted to alanine without any selection pressure for pyruvate synthesis from formate. Hence, this data confirms the activity of all three modules of RGP even in the presence of glucose. Further, ALE in glucose limiting conditions did not improve pyruvate flux via the RGP.
Growth characterization of these strains showed that the best growth rates were achieved in formate concentrations between 25 mM to 300 mM. Optimum growth required 5% CO2, and dropped when the CO2 concentration was reduced from 5% to 2.5%.
Whole-genome sequencing of these evolved strains revealed mutations in genes that encode Gdh1p, Pet9p, and Idh1p. These enzymes might influence intracellular NADPH, ATP, and NADH levels, indicating adjustment to meet the energy demand of the RGP. I reverse-engineered the GDH1 truncation mutation on unevolved serine biosensor strains and reproduced formate dependent growth. To elucidate the effect of the GDH1 mutation on formate assimilation, I reintroduced this mutation in the S288c strain and conducted carbon-tracing experiments to compared formate assimilation between WT and ∆gdh1 mutant strains. Comparatively, enhanced formate assimilation was recorded in the ∆gdh1 mutant strain.
Although the 13C carbon tracing experiments confirmed the activity of all three modules of the RGP, the overall pyruvate flux via the RGP might be limited by the supply of reducing power. Hence, in a different approach, I overexpressed the formate dehydrogenase (Fdh1p) for energy supply and serine deaminase (Cha1p) for active pyruvate synthesis in the S288c parental strain and established growth on formate and serine without glucose in the medium. Further reengineering and evolution of this strain with a consistent energy, and formate-derived serine supply for pyruvate synthesis, is essential to achieve complete formatotrophic growth in the yeast system.
To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli – which cannot naturally grow on formate – via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli. In the third chapter, I present the establishment of the serine threonine cycle (STC) – a synthetic formate assimilation pathway – in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) – a short, linear formate assimilation route – in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source.
NADPH is an essential cofactor that drives biosynthetic reactions in all living organisms. It is a reducing agent and thus electron donor of anabolic reactions that produce major cellular components as well as many products in biotechnology. Indeed, the engineering of metabolic pathways for the production of many products is often limited by the availability of NADPH. One common strategy to address this issue is to swap cofactor specificity from NADH to NADPH of enzymes. However, this process is time consuming and challenging because multiple parameters need to be engineered in parallel. Therefore, the first aim of this project is to establish an efficient metabolic biosensor to select enzymes that can reduce NADP+. An NADPH auxotroph strain was constructed by deleting major reactions involved in NADPH biosynthesis in E. coli’s central carbon metabolism with the exception of 6-phosphogluconate dehydrogenase. To validate this strain, two enzymes were tested in the presence of several carbon sources: a dihydrolipoamide dehydrogenase variant of E. coli harboring seven mutations and a formate dehydrogenase (FDH) from Mycobacterium vaccae N10 harboring four mutations were found to support NADPH biosynthesis and growth. The strain was subjected to adaptive laboratory evolution with the goal of testing its robustness under different carbon sources. Our evolution experiment resulted in the random mutagenesis of the malic enzyme (maeA), enabling it to produce NADPH. The additional deletion of maeA rendered a more robust second-generation biosensor strain for NADP+ reduction. We devised a structure-guided directed evolution approach to change cofactor specificity in Pseudomonas sp. 101 FDH. To this end, a library of >106 variants was tested using in vivo selection. Compared to the best engineered enzymes reported, our best variant carrying five mutations shows 5-fold higher catalytic efficiency and 13-fold higher specificity towards NADP+, as well as 2-fold higher affinity towards formate. In conclusion, we demonstrate the potential of in vivo selection and evolution-guided approaches to develop better NADPH biosensors and to engineer cofactor specificity by the simultaneous improvement of multiple parameters (kinetic efficiency with NADP+, specificity towards NADP+, and affinity towards formate), which is a major challenge in protein engineering due to the existence of tradeoffs and epistasis.
Natural products and their derivatives have always been a source of drug leads. In particular, bacterial compounds have played an important role in drug development, for example in the field of antibiotics. A decrease in the discovery of novel leads from natural sources and the hope of finding new leads through the generation of large libraries of drug-like compounds by combinatorial chemistry aimed at specific molecular targets drove the pharmaceutical companies away from research on natural products. However, recent technological advances in genetics, bioinformatics and analytical chemistry have revived the interest in natural products. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of natural products generated by the action of post-translationally modifying enzymes on precursor peptides translated from mRNA by ribosomes. The great substrate promiscuity exhibited by many of the enzymes from RiPP biosynthetic pathways have led to the generation of hundreds of novel synthetic and semisynthetic variants, including variants carrying non-canonical amino acids (ncAAs). The microviridins are a family of RiPPs characterized by their atypical tricyclic structure composed of lactone and lactam rings, and their activity as serine protease inhibitors. The generalities of their biosynthetic pathway have already been described, however, the lack of information on details such as the protease responsible for cleaving off the leader peptide from the cyclic core peptide has impeded the fast and cheap production of novel microviridin variants. In the present work, knowledge on leader peptide activation of enzymes from other RiPP families has been extrapolated to the microviridin family, making it possible to bypass the need of a leader peptide. This feature allowed for the exploitation of the microviridin biosynthetic machinery for the production of novel variants through the establishment of an efficient one-pot in vitro platform. The relevance of this chemoenzymatic approach has been exemplified by the synthesis of novel potent serine protease inhibitors from both rationally-designed peptide libraries and bioinformatically predicted microviridins. Additionally, new structure-activity relationships (SARs) could be inferred by screening microviridin intermediates. The significance of this technique was further demonstrated by the simple incorporation of ncAAs into the microviridin scaffold.
Macrophages in pathologically expanded dysfunctional white adipose tissue are exposed to a mix of potential modulators of inflammatory response, including fatty acids released from insulin-resistant adipocytes, increased levels of insulin produced to compensate insulin resistance, and prostaglandin E-2 (PGE(2)) released from activated macrophages. The current study addressed the question of how palmitate might interact with insulin or PGE(2) to induce the formation of the chemotactic pro-inflammatory cytokine interleukin-8 (IL-8). Human THP-1 cells were differentiated into macrophages. In these macrophages, palmitate induced IL-8 formation. Insulin enhanced the induction of IL-8 formation by palmitate as well as the palmitate-dependent stimulation of PGE(2) synthesis. PGE(2) in turn elicited IL-8 formation on its own and enhanced the induction of IL-8 release by palmitate, most likely by activating the EP4 receptor. Since IL-8 causes insulin resistance and fosters inflammation, the increase in palmitate-induced IL-8 formation that is caused by hyperinsulinemia and locally produced PGE(2) in chronically inflamed adipose tissue might favor disease progression in a vicious feed-forward cycle.