Regulation and function of nleB-like genes in Salmonella.
(bacterial genetics, infection biology, confocal microscopy)
(Contact Sébastien Lemire)
Carbonate anhydrase and virulence.
(bacterial genetics, infection biology, biochemistry)
(Contact Sébastien Lemire)
Characterization of the lysogenic switch of Salmonella prophages.
(microbial genetics, molecular biology, biochemistry)
(Contact Sébastien Lemire)
Tools for hightroughput generation of multiple mutants in Salmonella and other Gram-negative.
(molecular biology, bacterial genetics)
(Contact Sébastien Lemire)
Creation of single gene/multiple gene conditional knock-out mutant banks in the most relevant Salmonella serovars.
(molecular biology, bacterial genetics)
(Contact Sébastien Lemire)
Evolution of induction in Gifsy-like prophages.
(bacterial genetics, infection biology, biochemistry)
(Contact Sébastien Lemire)
Systems Biology and synthetic biology for sustainable production of biofuels and green chemicals
The conversion of biomass and various waste streams into biochemical building blocks and liquid biofuels for the transport sector has a great potential to substitute a significant proportion of the fossil fuels used today within the next decades. For these bioprocesses to become competitive with the petro-chemical processes, a high efficiency and low cost of all the steps from feedstock pre-treatment to product recovery processes is required.
In our group we use systems biology in combination with metabolic engineering and synthetic biology to improve bioconversion processes and to develop lactic acid bacteria and non-conventional yeasts into new production platforms for various biofuels and biochemicals.
Examples of our current activities that students are welcome to join include:
- Improving bacterial tolerance towards biofuels and lignocellulosic inhibitors inhibitors that arise during degradation of biomass to fermentable sugars. We use different approaches to attack this challenge:
o Adaptive evolution to obtain mutants with enhanced capability to grow in the presence of the inhibitory substance. Mapping of mutations using transcriptomics and genome sequencing/SNP analysis
o Mapping of cellular response towards sub-lethal concentrations of the inhibitory substance, using proteomics and transcriptomics
- Improving yeast and bacteria for degradation of alternative feedstocks such as C5 sugars from biomass and glycerol, a waste product from biodiesel production. Existing pathways are optimized and/or new pathways are introduced. Typically a project will include several of the following elements:
o Growth experiments, HPLC, enzymatic assays
o PCR, cloning, transformation, modulation of gene expression,
- Construction and improving yeast and bacteria for production of biofuels (ethanol, butanol, microdiesel) and green chemicals (lactic acid, 2,3-butanediol, C4-dicarboxylic acids), either by activating existing pathways or by introducing heterologous enzymes from other sources using metabolic engineering and synthetic biology. Typically a project will include the following elements:
o Growth/fermentation experiments, HPLC, enzymatic assays
o PCR, cloning, transformation, modulation of gene expression
(contact: Peter Ruhdal Jensen, )
Genotypic and Phenotypic Characterization of Pseudomonas Aeruginosa Isolates from CF Patients
Antibiotic sensitivity profiles of clinical isolates
High-troughput screening of our collection of P. Aeruginosa strains, isolated from >40 CF patients, for presence of phenotypic variations (for example decreased ability to create bio film, lowered production of virulence factors and quorum sensing molecules.) Interesting isolates need to be genotyped via DNA chips and relevant genes from isolates can be sequenced. (Contact: Søren Molin).
DNA microarray analysis on mutants of Lactococcus lactis with improved maltose metabolism
Maltose fermentation by L. lactis is slow due to an unknown limitation in the metabolic pathways but we have recently isolated a mutant of L. lactis capable of fermenting maltose at a much faster rate. In the proposed student project we will use DNA microarray analysis and genome sequencing to detect which enzymes may have been affected by the mutation and verify this by RT-PCR and enzymatic assays. Subsequently, the role of selected genes will be analysed by creating mutants with altered expression and studying the effect on maltose metabolism (contact: Christian Solem, ).
Control and regulation of fermentation mode in Lactococcus lactis
Depending on the sugar source and the conditions for growth, L. lactis can choose between different modes of fermentation with different patterns of by-products formed but it is still unclear how the shift in fermentation mode is achieved. In the proposed project we will compare glycolytic enzyme activities for cells grown on different sugar substrates and construct new and also use pre-existing mutants with altered activities of the glycolytic enzymes to determine their role in the metabolic shift (contact: Peter Ruhdal Jensen, ).
Control of sugar transport in Lactococcus lactis
Previous attempts to find the limiting factor(s) for the glycolytic flux in L. lactis have been unsuccessful despite overexpression of all individual steps in the glycolytic pathway. However, the limiting step could also be the transport of sugar into the cells which is carried out by various transport systems. In the student project we will change the capacity of the transport system by genetically increasing the transcription of the chromosomal genes encoding the transport systems and determine the effect on the transport of sugar into the cells (contact: Peter Ruhdal Jensen, ).
A Systems Biology approach to Salmonella infection
During the steps of infection a bacteria meets several challenges which can be overcome by expression of specific pathogenicity factors and otherwise adapting its cellular make-up. In collaboration with KU-Life (professor J.E. Olsen) and starting from published microarray data, the student project will aim at creating a series of mutants with varying promoter strength in potentially important virulence gene(s). Mutants will be characterized with regard to the ability to cause infection in cell culture assays. The overall aim is to elucidate the potential as targets for future interference strategies (contact: Moogens Kilstrup, mki).
Global regulatory network – The PyrR regulon
Lactococcus lactis will respond to the addition of exogenous pyrimidines by repressing the expression of the genes encoding the enzymes in the biosynthetic pathway. On the other hand, starvation for pyrimidines will result in an increase in the expression of the same genes. The genes encoding the enzymes in the pathway are subject to regulation at the transcriptional level by attenuators mediated by the regulatory protein PyrR. The details in the regulatory mechanism shall be elucidated. (Contact Jan Martinussen).
Global regulatory network – The PurR regulon in Lactobacillus plantarum
PurR mediates reulation of the purine biosynthetic genes. These genes are responsible for the biosynthesis of the purine nucleotide IMP through 11 enzymatic reactions. In Lactococcus lactis PurR is an transcriptional activator, whereas in other organisms PurR has been shown to act as a classical repressor. Preliminary studies in Lactobacillus plantarum have not revealed whether PurR is an activator or repressor in this organism. (Contact Jan Martinussen).
Transport and metabolism of exogenous nukleosides and nukleobases
Most organisms can transport and incorporate different intermediates in the nucleotide metabolism through the so-called salvage pathways. These pathways are important both for the exploitation of exogenous precursors and intracellular turn-over of RNA. In a broader perspective, it is important to know the details of the different salvage pathways as a number of different chemotherapeutical drugs are analogs of the intermediates in the nucleotide metabolism. As a model system the nucleotide metabolism in Lactococcus lactis is analyzed, using measurement of enzymatic activities, isolation of mutants, cloning and sequencing of relevant genes and physiological experiments with mutants. (Contact Jan Martinussen).
Lactic acid bacteria are not optimized for fast growth – Metabolic control analysis of the purine biosynthesis
All organisms can metabolize different intermediates in the nucleotide metabolism by the the salvage pathways. On the other hand, not all organisms can synthesize nucleotides de novo. Moreover, it has been shown that most – if not all – lactic acid bacteria have a partial purine requirement, meaning that they are not able to synthesize sufficient ATP and GTP when growing at their maximal growth rate. If shall be investigated whether to what extend a change of the expression of the purine biosynthetic genes affects the growth rate and the concentration of ATP and GTP. (Contact Jan Martinussen).
Metabolic control analysis of the pyrimidine biosynthesis
Nucleotides are – apart from being the building blocks of RNA and DNA – involved in virtually all biosynthetic pathways. In order to maintain homeostasis it is required that the cell keep a constant cellular nucleotide concentration. As a consequence, the cell must be able to adjust the flux through the biosynthetic pathway. Is it happening at a single step or is the controls dispersed over the entire pathway? Is the control at the genetic or enzymatic level? In this project the role of the individual steps in the pyrimidine biosynthetic pathway shall be investigated by metabolic control analysis. (Contact Jan Martinussen).