Join the Jung Lab
Contact email@example.com for possibilities to work on exciting projects as Postdoc, PhD student or undergraduate researcher.
We are looking for Master students (master thesis or lab rotations) working in the following areas:
1. Characterization of the novel acid resistance regulator MhpR
The DNA-binding transcriptional activator MhpR belongs to the IclR family and was recently identified by our group as major contributor to the acid stress response of Escherichia coli. Ribosome profiling and mRNA sequencing of cells exposed to pH 4.4 revealed that mhpR levels increase during acidification. mhpR knockout mutants show significantly reduced survival under severe acid stress. MhpR is involved in the degradation of phenylpropionate, but the connection to acid stress is currently unclear. The aim of this project is to elucidate the molecular mechanism of how MhpR and its target genes contribute to acid resistance in E. coli by using a variety of bioinformatics, biochemical and microbiological methods.
Please send your complete application in English as a single PDF (CV, motivation statement and research experience, record of study, certificates) to Prof. Dr. Kirsten Jung (firstname.lastname@example.org) .
2. New insights into the transcriptome of Escherichia coli by third generation sequencing
Third generation sequencing methods allow direct sequencing of RNA and DNA molecules without any bias or PCR. This approach helps tremendously in the identification and description of RNA molecules such as novel antisense RNAs, novel transcription start sites (TSSs), transcription termination sites, and operons. We have generated several datasets that require in-depth bioinformatics analysis.
The candidate should be enrolled in a Master Program in Bioinformatics (or equivalent). The candidate should be highly motivated and determined, with a strong interest in genomics and transcriptomics and the application of interdisciplinary approaches.
Experience in genome/transcriptome analysis and bioinformatics methods is required.
Please send your complete application in English as a single PDF (CV, motivation statement and research experience, record of study, certificates) to Prof. Dr. Kirsten Jung (email@example.com). In case of specific questions please contact Dr. Sebastian Riquelme-Barrios (S.Riquelme@biologie.uni-muenchen.de).
Duration: 6 months
3. Conformational changes underlying transcriptional regulation of Lys-R type regulators
The LysR-type transcriptional regulator (LTTR) family is one of the largest groups of bacterial transcription regulators, which are highly conserved among prokaryotes. They regulate a wide spectrum of cellular functions, as for example, oxidative stress response, virulence, motility and quorum sensing. LTTRs are unique in the sense that they function both as repressors and activators of single operonic genes. LTTRs show a conserved structure with an N-terminal DNA-binding domain (DBD) with a winged helix-turn-helix motif. Effector binding takes place at the C-terminal domain (EBD), which is linked to the DBD via a linker helix (see Figure on the left). The proteins form dimers and tetramers in solution, but are functionally active as tetramers when bound to dsDNA. On DNA they induce bending, which in turn facilitates recruitment of RNA polymerase. While there are some structures and structural models of LTTRs available (including their complexes with dsDNA), the concrete mechanism by which LTTRs use conformational changes, i.e., in the EBD, their quaternary structure or in the degree of DNA-bending, remain poorly understood.
The goal of this project is to investigate effector-induced conformational changes of an LTTR model system in the EBD (in its DNA-bound and unbound state), and to observe the degree of DNA bending under different conditions by biophysical techniques. ArgP from E. coli is a typical member of the LTTR family and controls the transcription of the argO gene encoding an exporter for arginine and canavanine to maintain an optimal ratio of intracellular arginine to lysine. We produced cysteine variants of ArgP that can be labelled with two fluorophores to monitor the conformational states of the EBDs via single-molecule FRET, smFRET (see Figure on the right). We further obtained fluorophore-labelled promoter DNA that will serve as a bending sensor when it interacts with wildtype ArgP. In the project, you will use established protocols to obtain the relevant ArgP variants, introduce fluorescence labels and perform biophysical assays. Biochemical properties of the system will be characterized by ligand-affinity measurements using calorimetry and microscale thermophoresis with the effectors arginine and lysine. Structural characterization of ArgP and its dsDNA complexes will be conduced via smFRET.
The work will be performed in the section “Microbiology” in collaboration between the groups of Kirsten Jung (Molecular Microbiology, firstname.lastname@example.org) and Thorben Cordes (Physical and Synthetic Biology, email@example.com). It is ideally suited for motivated students with an interest and background in microbiology, biochemistry, structural biology and biophysics.
 Schell, M. A., Molecular Biology of the LysR Family of Transcriptional Regulators. Annu. Rev. Microbiol. 47 (1993), pages 597–626.
 Zhou, X. et al., Crystal Structure of ArgP from Mycobacterium tuberculosis Confirms Two Distinct Conformations of Full-length LysR Transcriptional Regulators and Reveals Its Function in DNA Binding and Transcriptional Regulation. Journal of Molecular Biology 396 (2010), pages 1012–1024.
 Maddocks, S. E. et al., Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154 (2008), pages 3609–3623.
 Lerner, E. et al., Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 359 (2018), eaan1133