A position (E13 65%) for a doctoral researcher (m/f/d) is available in the group of Prof. Dr. Kirsten Jung at Ludwig-Maximilians-Universität München, Department of Microbiology, Germany.
Project: Methylation of mRNA is an important regulator of physiological processes in eukaryotes, but it has not been thoroughly studied in prokaryotes.
This project focuses on “The role of mRNA modification in the stress response of bacteria”. Working on the topic requires a combination of biochemical (RNA biochemistry) and microbiological techniques. It will be the task of the doctoral researcher to characterize the physiological significance of the m6A mRNA modification in bacteria under various stress conditions using systemic approaches, such as RNA-Seq, Ribo-Seq and proteomics. The project is funded by the DFG and embedded in the Collaborative Research Center (CRC) 1309 “Chemical Biology of Epigenetic Modifications”.
Requirements: The candidate should have an MSc. (or equivalent) in Life Sciences (Biochemistry, Chemistry, Biology, Microbiology). The candidate should be highly motivated and determined and have a strong interest in biochemistry and the application of interdisciplinary approaches.
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 (jung@lmu.de). In case of specific questions please contact Dr. Sebastian Riquelme-Barrios (S.Riquelme@biologie.uni-muenchen.de). Email: jung@lmu.de
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Current openings:
DOCTORAL POSITION in
Molecular Microbiology at the Ludwig-Maximilians-Universität München, Germany
A position (E13 65%) for a doctoral researcher
(m/f/d) is available in the group of Prof. Dr. Kirsten Jung at
Ludwig-Maximilians-Universität München, Department of Microbiology, Germany.
Project:
Methylation of mRNA is an important regulator of physiological processes in
eukaryotes, but it has not been thoroughly studied in prokaryotes.
This project focuses on “The role of mRNA modification in the stress
response of bacteria”. Working on the topic requires a combination of
biochemical (RNA biochemistry) and microbiological techniques. It will be the
task of the doctoral researcher to characterize the physiological significance
of the m6A mRNA modification in bacteria under various stress conditions using
systemic approaches, such as RNA-Seq, Ribo-Seq and proteomics. The project is
funded by the DFG and embedded in the Collaborative Research Center (CRC) 1309
“Chemical Biology of Epigenetic Modifications”.
Requirements: The
candidate should have an MSc. (or equivalent) in Life Sciences (Biochemistry,
Chemistry, Biology, Microbiology). The candidate should be highly motivated and
determined and have a strong interest in biochemistry and the application of
interdisciplinary approaches.
Qualifications:
Experience in RNA biochemical methods and bioinformatics are required.
Environment: The
Integrated Research Training Group 1309 (IRTG) provides a tailor-made training
environment for doctoral researchers active in the CRC on "Chemical
Biology of Epigenetic Modifications".
Please
send your complete application in English as a single PDF (CV,
motivation statement and research experience, record of study, certificates and
contact information of two referees) to Prof. Dr. Kirsten Jung (jung@lmu.de) until July 31, 2023.
Starting date: Oktober 1, 2023
Duration: 3 and half years (with the aim of completing the doctorate)
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 (jung@lmu.de) .
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.
Requirements:
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.
Qualifications:
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 (jung@lmu.de). 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.[1] 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.[2] 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[3]. 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.[4]
The work will be performed in the section “Microbiology” in collaboration
between the groups of Kirsten Jung (Molecular Microbiology, jung@lmu.de) and Thorben Cordes (Physical and
Synthetic Biology, cordes@bio.lmu.de).
It is ideally suited for motivated students with an interest and background in
microbiology, biochemistry, structural biology and biophysics.
References:
[1] Schell, M. A., Molecular Biology of the LysR Family of Transcriptional
Regulators. Annu. Rev. Microbiol. 47 (1993), pages 597–626.
[2] 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.
[3] Maddocks, S. E. et al., Structure and function of the LysR-type
transcriptional regulator (LTTR) family proteins. Microbiology 154 (2008),
pages 3609–3623.
[4] Lerner, E. et al., Toward dynamic structural biology: Two decades of
single-molecule Förster resonance energy transfer. Science 359 (2018), eaan1133
Supervisor website:
Prof. Dr. Kirsten Jung - Mikrobiologie - LMU München (uni-muenchen.de)
Kirsten Jung - Google Scholar
AG "Molekulare Mikrobiologie" (Prof. Dr. K. Jung) - Mikrobiologie - LMU München (uni-muenchen.de)
Prof. Dr. Kirsten Jung - Center for Advanced Studies LMU (CAS) - LMU Munich (uni-muenchen.de)
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