Exploiting combinatorial cultivation conditions to infer transcriptional regulation

BACKGROUND: Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the generated regulatory network, they are usually lacking. This is due to the fact that the large heterogeneity in the employed conditions and the continuous changes in environmental parameters in the often used shake-flask cultures, prevent the unambiguous modeling of the cultivation conditions within the computational framework. RESULTS: We designed an experimental setup that allows us to explicitly model the cultivation conditions and use these to infer the activity of TFs. The yeast Saccharomyces cerevisiae was cultivated under four different nutrient limitations in both aerobic and anaerobic chemostat cultures. In the chemostats, environmental and growth parameters are accurately controlled. Consequently, the measured transcriptional response can be directly correlated with changes in the limited nutrient or oxygen concentration. We devised a tailor-made computational approach that exploits the systematic setup of the cultivation conditions in order to identify the individual and combined effects of nutrient limitations and oxygen availability on expression behavior and TF activity. CONCLUSION: Incorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions. For example, our results confirm the established role of TF Hap4 in both aerobic regulation and glucose derepression. Among the numerous inferred condition-specific regulatory associations between gene sets and TFs, also many novel putative regulatory mechanisms, such as the possible role of Tye7 in sulfur metabolism, were identified

Transcriptional profiling of Aspergillus niger

The industrially important fungus Aspergillus niger feeds naturally on decomposing plant material, of which a significant proportion is lipid. Examination of the A. niger genome sequence suggested that all proteins required for metabolic conversion of lipids are present, including 63 predicted lipases. In contrast to polysaccharide-degrading enzyme networks, not much is known about the signaling and regulatory processes that control lipase expression and activity in fungi. This project was aimed to gain better understanding of lipid degradation mechanisms and how this process is regulated in A. niger, primarily via assessment of its gene transcription levels. Minimizing biological and technical variation is crucial for experiments in which transcription levels are determined, such as microarray and quantitative real-time PCR experiments. However, A. niger is difficult to cultivate in a reproducible way due to its filamentous growth. In addition, the complex processing steps of transcriptomics technologies add non-experimental variation to the biological variation. To reduce this data noise, robust protocols based on a batch-fermentation setup were developed. Variation in this setup was surveyed by examining the fungal transcriptional response towards a pulse of D-xylose. The sources of non-experimental variation were described by variance components analysis. Two-thirds of total variation stems from differences in routine handling of fermentations, but in absolute terms this variation is low. As D-xylose is an inducer of the xylanolytic system, the high reproducibility of cultures for the first time allowed a detailed description of the global fungal transcriptional response towards D-xylose using microarrays. The transcriptional response towards three plant derived oils was examined in another study. Both olive oil and a wheat-gluten extracted oil induce the transcription of genes involved in lipid metabolism and peroxisome assembly, albeit with different expression profiles. The third oil, a plant membrane lipid, did not trigger a transcriptional response. Microarray data are related to the physiology of the fungus. To better understand the general principles that underlie gene regulation and gene transcription, microarray data from cultures grown under mildly and strongly perturbed conditions were analyzed for co-expression of genes. Despite the diverse culturing conditions, co-expressed gene modules could be identified. Some of these modules can be related to biological functions. For some modules, conserved promoter elements were identified, which suggests that genes in these modules are regulated on a transcriptional level. The work described in this thesis shows that (i) high-quality -omics data for A. niger can be generated; that (ii) analysis and interpretation of these data enhances our understanding of the xylanolytic and lipid metabolic regulons; and (iii) that these data give insight into the regulatory mechanisms of this fungus. <br/

Optimisation of the production of cathepsin L1 from a recombinant saccharomyces cerevisiae

Cathepsin L1 is a cysteine protease that has been previously isolated and functionally expressed in Saccharomyces cerevisiae. It has the potential to be employed as a vaccine for liver-fluke disease in cattle and other ruminants. Production of this recombinant enzyme, which is secreted into the media from recombinant yeast, was studied initially in shake flask cultures and subsequently in 5L and 15L fermenters. In early studies, low productivity and especially variations in Cathepsin L1 production was a significant problem. A standard operating protocol (SOP) has been designed to consistently supply an optimum inoculum for large-scale fermentations. This SOP which involved 'blending' colonies for inoculum cultures in conjunction with sub-culturing starter flasks for two successive cycles of 48 hours, proved to be the most successful for consistently high levels of enzyme production during the ensuing fermentation. The pH and temperature optima are pH 6.5 and 30°C respectively for culturing the recombinant yeast to produce both both high biomass levels and high enzyme activity. Addition of casamino acids to the selective media or replacing it with complex YEPD resulted in poor plasmid stability and low Cathepsin L1 production. By supplementing the selective media with extra yeast nitrogen base, using a glucose concentration of 20g/L, enzyme activity increased by 3-4 fold and much higher levels of plasmid stability than observed in non-selective media were sustained. Enzyme activity of 0.74 units/mL were obtained in supplemented media compared to 0.19 units/mL in selective media. Investigations were performed on the constitutive behaviour of the ADH1 promoter, which controls the expression of Cathepsin L1 in this recombinant yeast strain. It revealed that enzyme production is repressed at high concentrations of glucose but gradually increases as glucose is utilised. Cathepsin L1 is still expressed during the ethanol consumption phase, albeit at a slower rate than during the latter stages of glucose consumption

Developing a lactate-inducible transgene expression system for use in Chinese hamster ovary cells

The accumulation of lactate during cultivation of mammalian cells for biopharmaceutical production is a longstanding issue affecting glycosylation quality and productivity. Many approaches exist to mitigate its impact, either through the replacement of glucose with slowly metabolised sugars, dynamic feeding strategies, or host cell engineering. The manipulation of genes in this latter approach is constitutive and may suboptimally respond to cellular needs. The LldR proteins from Corynebacterium glutamicum and Pseudomonas aeruginosa have been used in this project to create a lactate-inducible transgene expression system, which can be used subsequently to dynamically drive expression of proteins previously targeted to mitigate the accumulation of lactate. Expression and purification of these LldR proteins, fused to transcriptional effector domains in various orientations and with fusion linkers in certain cases, allowed in vitro characterisation and optimisation of the constituent parts of the inducible system. This provided crucial information in some cases about the need to use a flexible linker between LldR and a VP64 transactivation domain. In vivo experimentation of these optimised systems showed significant levels of induction in response to 20 mM lactate, with a 3.46-fold decrease in expression seen for one construct. Some preliminary work was also carried out with Cas9-VPR, which was shown to be able to upregulate transiently transfected genes up to 1.6-fold. In the future, this will be a useful tool for upregulating multiple previously identified targets, as well as helping to find new beneficial targets. The general approach outlined here for the development of this lactate-inducible transgene expression system will be appropriate for any other such project where the ligand of interest is a central metabolite. Inherently weaker induction might be a feature of such a system, given the presence of the inducer at low and relatively benign or neutral concentrations throughout a period of interest; testing an unoptimised system in mammalian cells may return little or no detectable induction signal and therefore it will not be straightforward to optimise such a system solely through the use of in vivo experimentation. In vitro characterisation of the inducible system components, as performed here, can provide essential feedback regarding the impact of effector domain fusion and operator design on the DNA-binding affinity of the biosensor prior to in vivo testing. The work in this thesis will allow the future exploration of dynamically regulated host cell engineering designed to combat the lactate accumulation phenotype.Open Acces

Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of ‘intelligent’ metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.IS

Impact of xylose and mannose on central metabolism of yeast Saccharomyces cerevisiae

In this study, understanding of the central metabolism was improved by quantification of metabolite concentrations, enzyme activities, protein abundances, and gene transcript concentrations. Intracellular fluxes were estimated by applying stoichiometric models of metabolism. The methods were applied in the study of yeast Saccharomyces cerevisiae in two separate projects. A xylose project aimed at improved utilization of D-xylose as a substrate for, e.g., producing biomaterial-based fuel ethanol. A mannose project studied the production of GDP-mannose from D-mannose in a strain lacking the gene for phosphomannose isomerase (PMI40 deletion). Hexose, D-glucose is the only sugar more abundant than pentose D-xylose. D-xylose is common in hardwoods (e.g. birch) and crop residues (ca. 25% of dry weight). However, S. cerevisiae is unable to utilize D-xylose without a recombinant pathway where D-xylose is converted to D-xylulose. In this study D-xylose was converted in two steps via xylitol: by D-xylose reductase and xylitol dehydrogenase encoded by XYL1 and XYL2 from Pichia stipitis, respectively. Additionally, endogenous xylulokinase (XKS1) was overexpressed in order to increase the consumption of D-xylose by enhancing the phosphorylation of D-xylulose. Despite of the functional recombinant pathway the utilization rates of D-xylose still remained low. This study proposes a set of limitations that are responsible for the low utilization rates of D-xylose under microaerobic conditions. Cells compensated for the cofactor imbalance, caused by the conversion of D-xylose to D-xylulose, by increasing the flux through the oxidative pentose phosphate pathway and by shuttling NADH redox potential to mitochondrion to be oxidized in oxidative phosphorylation. However, mitochondrial NADH inhibits citrate synthase in citric acid cycle, and consequently lower flux through citric acid cycle limits oxidative phosphorylation. Further, limitations in the uptake of D-xylose, in the pentose phosphate pathway, and in the citric acid cycle were alleviated in xylose chemostat isolates with three-fold improved xylose utilization rates. Uptake rate of D-xylose, assayed in vitro with radioactive D-xylose, was improved by 60% in the chemostat isolates grown under aerobic conditions on D-xylose. In the pentose phosphate pathway activities of transketolase and transaldolase were increased two-fold, and consequently concentrations of their substrates were decreased two-fold in the chemostat isolates. Finally, less pyruvate and citrate, but more malate accumulated in the chemostat isolates than in the original strain grown on D-xylose under aerobic conditions. In a S. cerevisiae strain with PMI40 deletion, growth on media without D-mannose and D-glucose is disabled. Phosphomannose isomerase encoded by PMI40 connects D-mannose to glycolysis, which is the main pathway for D-glucose utilization. Hypothetically, a PMI40 deletion strain would direct all its D-mannose into the biosynthesis of GDP-mannose. However, in the PMI40 deletion strain increased initial D-mannose concentrations led to increased intracellular mannose 6-phosphate concentrations. Mannose 6-phosphate inhibited activity of phosphoglucose isomerase (encoded by PGI1) in glycolysis, which in essence is equivalent to suppressed expression of PGI1. Subsequently, reduced availability of glycolysis intermediates, due to inhibition of phosphoglucose isomerase, led to a decrease in the glycolytic flux. Eventually, increased initial D-mannose concentrations resulted in a starvation response, which was accompanied by slower cell cycle and slower growth rate.reviewe