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Doctoral Projects 2017

Doctoral projects offered by LSM faculty members to applicants for 2017:

Attention: The LSM portal remained open until 18:00 CET, on the December 7th, since the website was experiencing an overload due to last minute submissions.

Please note

  • You have to apply with our online application tool.
  • The deadline to submit your application is the 7th of December 2016, 18:00 CET.
  • Please inform your referees as soon as possible to get their affirmation to write a recommendation on your behalf, the deadline for the letters of reference is the 13th of December 2016, 12:00 CET.
  • Please click on the name of the supervisor to get redirected automatically to further information on the research group and the scientific contents. 

Supervisor: PD Dr. Bettina BOELTER (Plant Sciences, Biochemistry, Molecular Biology)

Acclimation in chloroplast protein import

Short term acclimation of chloroplasts to various environmental triggers requires drastic changes in their proteome composition. For example, the amount of photosynthetic complexes needs to be adapted in response to varying light intensities or temperature to ensure optimal performance. Since the majority of chloroplast proteins is encoded in the nucleus and translated as preproteins in the cytosol, posttranslational targeting is a first crucial step towards providing these organelles with the required proteins. To enter the chloroplast, preproteins have to cross the double envelope membrane, which is facilitated by two complex translocation machineries responsible for preprotein recognition and transport. The import process itself is highly regulated at different levels from the outside as well as the inside of the organelle where distinct signalling cascades lead to dynamic acclimation of import activity.
In the proposed project we want to address the following questions:
I. How is thiol and redox mediated import acclimation integrated into cell signalling?
II. Which novel components participate in modulating the transport processes?
To this end, we will combine classical biochemistry and cell biology methods with novel genetic approaches.

For more information please refer to:
Bölter B, Soll J, Schwenkert S. Redox meets protein trafficking. Biochim Biophys Acta (2015) 1847(9):949-56. doi: 10.1016/j.bbabio.2015.01.010

 Supervisor: Prof Michael BOSHART (Genetics, Biochemistry and Cell Biology)

Title : Host adaptation and differentiation of Trypanosoma

The protozoan pathogen Tryoanosoma is transmitted by blood-sucking Tsetse flies and undergoes a complex development to adapt to different physical and nutritional environments in fly organs. We study the interplay between metabolic cues and signaling pathways that control stage differentiation and social motility of the parasites and ultimately transmission of the pathogen. The PhD project will either focus on parasite adenyl cyclases and their downstram effectors or on the link between citrate metabolism, gluconeogenesis and transmission. A large collection of knock-out mutants of relevant proteins is available and collaborations are established for fly transmission and for metabolite and flux analysis by MS. The project is embedded in a collaborative network with teams in France, Belgium and Japan. Possible outcomes of the project include innovative strategies to disrupt the infectious cycle of parasites causing neglected tropical diseases in humans and domestic animals .


Gould MK, Bachmaier S, et al. (2013) Antimicrob Agents Chemother 57: 4882-4893
Allmann, S. et al. (2013) J Biol Chem 288, 18494-18505
Salmon D, Vanwalleghem G, et al. (2012) Science 337: 463-466
Salmon D, Bachmaier S, et al. (2012) Mol Microbiol 84: 225-242

*The candidate is expected to apply for a fellowship.


Supervisor: PD Dr. Dr. Christian GRIMM (Pharmacology, Molecular Biology)

Title: Known and novel members of the endolysosomal transportome/channelome as candidates to rescue loss of TRPML1 function in MLIV patients

Aim of this project is to explore novel therapeutic strategies for mucolipidosis type IV (MLIV), a lysosomal storage disorder that is caused by loss or dysfunction of the EL cation channel TRPML1. One focus is on the identification and characterization of surrogates for TRPML1 in the EL channelome/transportome members of which, when specifically stimulated may compensate for the loss of TRPML1 (e.g. two-pore cation channels, CLN proteins, MFSD proteins and others). A second attempt is the identification of small molecule activators/modulators for the afore identified TRPML1 surrogates in high-throughput screens.
Human MLIV patient and wildtype (WT) cells (e.g. fibroblasts) as well as primary murine TRPML1 knockout and WT cells (e.g. neurons) will be used to assess potential rescue effects of putative surrogates for TRPML1 and small molecule activators. Their rescue potential will be analyzed by applying the endolysosomal patch-clamp technique as well as biochemical and microscopy approaches. Finally, the (patho)physiological effects of TRPML1-surrogate proteins and small molecule activators will be assessed in in–vivo experiments. Following validation, identified small molecule activators will be administered to TRPML1 knockout mice and WT mice and will be tested for amelioration of motoric performance, neurological functions and life span.


Project-related literature from our laboratory Grimm C, Jörs S, Saldanha SA, Obukhov AG, Pan B, Oshima K, Cuajungco MP, Chase P, Hodder P,
Heller, S (2010) Small molecule activators of TRPML3. Cell Chem. Biol., 17: 135-148
Grimm C, Holdt LM, Chen C-C, Hassan S, Müller C, Jörs S, Cuny H, Kissing S, Schröder B, Butz E, Northoff B, Castonguay J, Luber CA, Moser M, Spahn S, Lüllmann-Rauch R, Fendel C, Klugbauer N, Griesbeck O, Haas A, Mann M, Bracher F, Teupser D, Saftig P, Biel M, Wahl-Schott C (2014) High susceptibility to fatty liver disease in two-pore channel 2-deficient mice. Nature Commun, 5:4699
Chen, C-C, Keller, M, Hess, M, Schiffmann, R, Urban, N, Wolfgardt, A, Schaefer, M, Bracher, F, Biel, M, Wahl-Schott, C, Grimm, C (2014) A small molecule restores function to TRPML1 mutant isoforms responsible for mucolipidosis type IV. Nature Commun, 5: 4681
Sakurai, Y, Kolokoltsov, AA, Chen, C-C, Tidwell, MW, Bauta, WE, Klugbauer, N, Grimm, C, Wahl-Schott, C, Biel, M, Davey, RA (2015) Two pore channels control Ebolavirus host cell entry and are drug targets for disease treatment, Science, 347: 995-998

Supervisor: Prof. Kirsten JUNG (Microbiology, Cell Biology, Biochemistry)

Title : Influence of protein sequence and mRNA modification on the stress resistance of Escherichia coli

Enterobacteriaceae, such as Escherichia coli, are exposed to extremely low pH in the stomach (HCl, pH <2.5), and low pH values in the gut (short-chain carboxylic acids). To survive these bacteria are able to induce various decarboxylase systems. We have been working on the elucidation of the structure and molecular function of the lysine-dependent Cad-system in E. coli [1-4].

In this project we will focus on another acid stress decarboxylase system, the glutamate–dependent Gad-system. The Gad-system consists of the glutamate decarboxylases GadA and GadB and the antiporter GadC. The activation of gadBC and gadA genes is very complex [5]. Moreover, the mRNAs gadB, gadC und gadA were found to be m6A modified [6].

It is the aim of the project to analyze the influence of protein sequence and m6A modifications on the Gad-acid stress system. Moreover, m6A mRNA-binding proteins shall be identified. Finally, mRNA modifications in different strains of E. coli (laboratory strains, pathogens and commensals) shall be systematically analyzed and compared.

Experience and expertise in microbiological, molecular and bioinformatic techniques as well as a strong interest for systemic, e.g. methylomes studies are required.

[1] Fritz, G., Koller, C., Tetsch, L., Haneburger, I., Burdack, K., Jung, K., Gerland, U. (2009) J. Mol. Biol. 393, 272–286.
[2] Haneburger, I., Eichinger, A., Skerra, A., Jung, K., (2011) J. Biol. Chem. 286, 10681-10689.
[3] Haneburger, I., Fritz, G., Jurkschat, N., Tetsch, L., Eichinger, A., Skerra, A., Gerland, U., Jung, K. (2012) J. Mol. Biol. 424, 15-27.
[4] Buchner, S., Schlundt, A., Lassak, J., Sattler M., Jung, K. (2015) J. Mol. Biol. 427, 2548-2561.
[5] Gong, S.M., Ma, Z., Foster, J.W. (2004) Mol. Microbiol. 54, 948-961.
[6] Deng, X., Chen, K., Luo, GZ., Weng, XC., Ji, QJ., Zhou, TH., He, C. (2015) Nucleic Acids Res. 43, 6557-6567.

Supervisor: Prof. Heinrich JUNG (Microbiology, Cell Biology, Biochemistry)

Title: Significance and function of SSS family-related signal transduction systems in pathogenic and non-pathogenic Pseudomonas species

The solute/sodium symporter (SSS) family (TC 2A.21, SLC5) comprises integral membrane transport proteins that use an electrochemical sodium gradient to drive the uptake of various organic and inorganic solutes into cells (Jung, 2002). Our previous work focused on the elucidation of the significance and molecular mechanism of function of transporters of this family using a combination of microbiological, biochemical and spectroscopic methods (e.g., (Bracher et al., 2016; Li et al., 2015; Raba et al., 2014).
A new project aims at the characterization of an unusual type of bacterial sensor kinase systems that is characterized by a N-terminal domain which is similar to members of the SSS family (e.g., PanF and PutP) at the structural level while the C-terminal domain shares homology to histidine kinases (e.g., NtrB) (Jung, 2002). Proteins exhibiting such a domain composition are found in proteobacteria of the subgroups alpha, gamma and delta (e.g., the putative proline sensor PrlS of Aeromonas hydrophila, CbrA of Pseudomonas aeruginosa). CbrA functions together with its cognate response regulator, CbrB, and plays an important role in nutrient acquisition (Nishijyo et al., 2001). Recently it was shown that the SSS domain of CbrA of P. fluorescencs is capable of transporting the amino acid histidine (Zhang et al., 2015).
Tasks of the Ph.D. thesis involve the detailed investigation of two different SSS family-related signal transduction systems that are found in both the opportunistic pathogen P. aeruginosa and the soil bacterium Pseudomonas putida. The relevance of these systems for bacterial physiology and virulence shall be explored. Since the mode of action of these systems is still enigmatic, an additional focus of the project will be on the elucidation of the molecular mechanism of function of the sensory systems.
Candidates should have profound knowledge and experimental expertise in microbiological, biochemical and bioinformatic methods and techniques.

Bracher S, Guerin K, Polyhach Y, Jeschke G, Dittmer S, Frey S, Bohm M, and Jung H. 2016. Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure. J Biol Chem 291:4998-5008. doi: 10.1074/jbc.M115.675306
Jung H. 2002. The sodium/substrate symporter family: structural and functional features. FEBS Lett. 529:73-77. doi:
Li Z, Lee AS, Bracher S, Jung H, Paz A, Kumar JP, Abramson J, Quick M, and Shi L. 2015. Identification of a second substrate-binding site in solute-sodium symporters. J. Biol. Chem. 290:127-141. doi: 10.1074/jbc.M114.584383
Nishijyo T, Haas D, and Itoh Y. 2001. The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa Mol.Microbiol. 40:917-931. doi:
Raba M, Dunkel S, Hilger D, Lipiszko K, Polyhach Y, Jeschke G, Bracher S, Klare JP, Quick M, Jung H, et al. 2014. Extracellular loop 4 of the proline transporter PutP controls the periplasmic entrance to ligand binding sites. Structure 22:769-780. doi: 10.1016/j.str.2014.03.011
Zhang XX, Gauntlett JC, Oldenburg DG, Cook GM, and Rainey PB. 2015. Role of the Transporter-Like Sensor Kinase CbrA in Histidine Uptake and Signal Transduction. J Bacteriol 197:2867-2878. doi: 10.1128/JB.00361-15

Supervisor: Dr Macarena MARÍN (Plant Sciences, Biochemistry, Genetics)

Title: Identification of novel legume genes required for symbiotic compatibility

To overcome nitrogen limitation legumes symbiotically associate with nitrogen-fixing rhizobia. Compatible associations result in the intracellular accommodation of the bacterial symbiont inside the inner cells of a specialised organ, called the root nodule. Poorly compatible associations can result in nodule organogenesis. However, these often exhibit suboptimal rhizobia infection and reduced nitrogen fixation, which leads to a decreased plant yield (Melino et al., 2012). Rhizobial Nod factors and their plants receptors are key determinants of symbiotic recognition and compatibility at the root epidermis (Radutoiu et al., 2003; Radutoiu et al., 2007). However, there is accumulating evidence that the compatibility between symbionts is a more complex trait than previously thought. Not only additional molecules, such as secreted effector proteins, exo- and lipopolysachharides, cyclic glucans modulate compatibility (Reviewed in (Wang et al., 2012), but also distinct compatibility check-points along the infection process have been identified (Madsen et al., 2010). To identify novel genes determining compatibility, we will exploit the phenotypic variation of a collection of Lotus japonicus ecotypes in response to Rhizobium leguminosarum strains, which not only can associate with multiple Lotus species, but induces distinct species- and ecotype-specific nodulation phenotypes (Gossmann et al., 2012).
The aim of this project is to identify and characterise novel genes determining symbiotic compatibility between rhizobia and legumes. Candidate genes identified by quantitative trade locus (QTL) analysis and Genome-wide association studies (GWAS) will be validated by genome-editing (CRISPR/Cas9) and the encoded proteins will be characterised by cell biological and biochemical methods. With this we aim to expand our understanding of compatibility, one of the major limitations for yield improvement in agricultural fields.


Gossmann, J.A., Markmann, K., Brachmann, A., Rose, L.E., and Parniske, M. 2012. Polymorphic infection and organogenesis patterns induced by a Rhizobium leguminosarum isolate from Lotus root nodules are determined by the host genotype. New Phytol 196:561-573.
Madsen, L.H., Tirichine, L., Jurkiewicz, A., Sullivan, J.T., Heckmann, A.B., Bek, A.S., Ronson, C.W., James, E.K., and Stougaard, J. 2010. The molecular network governing nodule organogenesis and infection in the model legume Lotus japonicus. Nat Commun 1:10.
Melino, V.J., Drew, E.A., Ballard, R.A., Reeve, W.G., Thomson, G., White, R.G., and O'Hara, G.W. 2012. Identifying abnormalities in symbiotic development between Trifolium spp. and Rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes. Ann Bot 110:1559-1572.
Radutoiu, S., Madsen, L.H., Madsen, E.B., Jurkiewicz, A., Fukai, E., Quistgaard, E.M., Albrektsen, A.S., James, E.K., Thirup, S., and Stougaard, J. 2007. LysM domains mediate lipochitin-oligosaccharide recognition and Nfr genes extend the symbiotic host range. Embo J 26:3923-3935.
Radutoiu, S., Madsen, L.H., Madsen, E.B., Felle, H.H., Umehara, Y., Gronlund, M., Sato, S., Nakamura, Y., Tabata, S., Sandal, N., and Stougaard, J. 2003. Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature 425:585-592.
Wang, D., Yang, S., Tang, F., and Zhu, H. 2012. Symbiosis specificity in the legume: rhizobial mutualism. Cell Microbiol 14:334-342.



Supervisor: PD. Dr. Stylianos MICHALAKIS (Pharmacology, Gene therapy)

Title: Develompment of novel AAV vectors for improved retinal gene therapy

Recombinant adeno-associated virus (rAAV) vectors have become the “gold standard” gene delivery tool for targeting retinal cells. rAAV-based vectors were tested in a number of human clinical trials and have proven safe for the use in the retina. For efficient transduction the current rAAV vector technology requires delivery of the AAV vectors directly to the target cell surface. Direct exposure of the rAAV vectors to the target cell types (retinal photoreceptors) can only be achieved by surgical detachment of the neuroretina from the retinal pigment epithelium (RPE) and delivery of the vectors into this temporally formed subretinal compartment (= subretinal injection). However, subretinal injections result only in a very localized transduction of retinal cells within the subretinal bleb area since (i) AAVs are not able to penetrate well into deeper levels of the retinal tissue and (ii) cells outside the bleb are not exposed to sufficient amounts of the vector.
Therefore, there is a critical unmet need to develop novel AAV vectors with improved transduction properties that enable transretinal gene expression through less invasive routes of delivery (e.g. intravitreal injection).
This projects aims at generating and evaluating using state-of-the-art virological, biochemical, genetic, cell biological and gene transfer methods in relevant in vitro and/or in vivo models (from various species e.g. mouse, dog, pig, NHP, human).

Supervisor: Prof. Joerg NICKELSEN (Plant Sciences, Biochemistry, Genetics)

Title: Regulation of chloroplast gene expression in Chlamydomonas.

Due to the endosymbiotic evolutionary history of chloroplasts, most of the multimeric plastid protein complexes are formed by subunits which are encoded by either the nuclear or the chloroplast genome. This intrinsic complicated situation has led to the development of a coordination system for gene expression in both cellular compartments as well as a chloroplast biogenesis machinery that ensures the ordered step-wise assembly of photosynthetic complexes within the organelle. Moreover, both processes appear to be interlinked via feed-back control mechanisms that involve the sensing of non-assembled complex subunits. Accumulating evidence  indicate that numerous factors are involved in these regulatory processes. Some of which share characteristic motifs like e.g. TPR, PPR and other repeat domains or possess classical RNA binding domains and are typically organized in high-molecular weight complexes [Schwarz et al. (2007) Plant Cell 19: 3627-3639; Johnson et al. (2010) Plant Cell 22: 234-248]. This project aims at elucidating the molecular function of nucleus-encoded proteins potentially being involved in the biogenesis of thylakoid membranes in the model system Chlamydomonas reinhardtii.

Supervisor: Prof. Martin PARNISKE (Genetics, Biochemistry, Cell Biology)

Title: Molecular inventions underlying the evolution of the nitrogen-fixing root nodule symbiosis

Crop production worldwide is sustained through nitrogen fertilizer produced via the energy-demanding Haber-Bosch process. One group of closely related plants evolved to become independent of nitrogen from the soil by engaging in symbiosis with bacteria that convert atmospheric nitrogen to plant-usable ammonium and are hosted within specialized organs, the root nodules. Nodulation evolved several times independently but exclusively in four related orders, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo) based on a putative genetic predisposition to evolve root nodules acquired by a common ancestor of this clade.
The doctoral project will contribute to a larger ongoing effort of the Parniske lab to identify the elusive genetic switches involved in the evolution of nodulation. It builds on the underlying idea that a succession of events co-opted preexisting developmental programs to be activated by symbiotic stimuli. We will systematically investigate and compare the prewired connections between signaling pathways and developmental modules present in non-nodulating and nodulating relatives, to identify components acquired by nodulators. The Rosaceae represent a particularly attractive family to test evolutionary hypotheses by transferring candidate switches from a nodulator into the genome of closely related sister genera to enable nitrogen fixing root nodule symbiosis. Most genera of the Rosaceae including economically valuable targets such as apple and strawberry are non-nodulating. A minority of Rosaceae form ancestral, lateral root related actinorhiza nodules with Frankia actinobacteria, which differs from the derived, more complex symbiosis of legumes with rhizobia. Frankia strains have a very broad host range and can fix nitrogen at ambient oxygen concentrations thus imposing minimal constraints on a host environment suitable for efficient symbiosis. Thus, by retracing small evolutionary steps within the Rosaceae we will take a huge leap towards nitrogen-fertilizer independent crops for sustainable agriculture.


Supervisor: PD Dr. Serena SCHWENKERT (Plant Sciences, Biochemistry, Molecular Biology)

Title: Chaperones and TPR proteins in organellar protein import and chloroplast biogenesis.

SerenaIn the eukaryotic cell most organellar proteins are synthesized as preproteins in the cytosol and are either post- or co-translationally translocated into chloroplasts, mitochondria or the endoplasmic reticulum. During posttranslational protein transport the preproteins have to be kept in an import competent state and molecular crowding has to be prevented, since this can easily lead to misfolding or aggregation. This process is assisted by the molecular chaperones HSP90 and HSP70, which also mediate interaction of preproteins with the membrane surfaces. This interaction is conferred by tetratricopeptide repeat (TPR) proteins, which are associated with the translocon complexes. The aim of this project is to characterize the molecular and regulatory function of these TPR docking proteins during posttranslational protein transport. The functional and structural analyses of these docking proteins will not only provide insight into the import mechanism of preproteins but also elucidate the role of chaperones and the respective receptors in specific targeting of preproteins. Moreover, not only the cytosolic, but also the chloroplast resident TPR proteins as well as HSP90 are indispensable for chloroplast biogenesis. We will therefore investigate the composition and mode of action of the chloroplast HSP90 machinery, with special focus on its conformational dynamics in comparison with the cytosolic localized chaperone setup. To this end we will apply a variety of biochemical and molecular biological techniques, such as protein purification, co-immunoprecipitation and expression of fluorescent proteins.

For further information see:

Supervisor: Dr. Arne WEIBERG (Genetics, Plant-Microbe Interaction, Small RNA Biology)

Title: The role of small regulatory RNAs in plant-microbe interactions.

Small RNAs direct gene silencing through a mechanism called RNA interference (RNAi). Mobile small RNAs are exchanged between organisms and trigger cross-kingdom RNA silencing during host-microbe interactions. As a virulence strategy, Botrytis cinerea produces mobile small RNAs during host plant infection that hijack the host RNAi pathway and silence important plant immunity genes (Weiberg et al. Science 2013, 342:118-23). We use B. cinerea and the oomycete Hyaloperonospora arabidopsidis as our pathogen model systems. Understanding molecular aspects that determine cross-kingdom RNAi is the aim of this doctoral project. This is of enormous interest for the implementation of RNAi-based crop protection strategies.

For further information see: