LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Genetics
Subject areas/Research fields: Plant Sciences, Genetics, Molecular Biology, Computational Biology
Keywords: gene regulation; plant-plant interaction; elicitor
Name of supervisor: Prof. Dr. Claude Becker
Project title: Induction of defence compounds in rice by fungal elicitors
Project description: Plants mostly grow in dense communities, together with plants from the same or a different species. Because resources are scarce, plants must compete with their neighbours for nutrients, space, and water. Some plant species, including important crops such as rice, release chemical compounds to inhibit the growth of neighbours and to defend themselves against various pests.
Upon perceiving a chemical trigger, rice plants produce and release a particular type of diterpenes, momilactone A and B, that act against fungal pathogens as well as against non-kin plant species (Serra Serra et al. 2021). In this project, our goal is to identify the molecular trigger(s), the mechanism by which they are perceived, and the signalling cascade that ultimately leads to the enhanced production and release of the compounds.
To this end, we employ a combination of genetics, genomics, biotechnology, and metabolomic analyses. In collaboration with microbiologists and biochemists, we will test an array of fungal extracts and filtrates from both beneficial and pathogenic fungi; via iterative fractionations and purifications, we aim to identify the specific molecules that trigger the response. Using reporter lines, mutant collections, and CRISPR/Cas9 technology, we will then focus on identifying the components of the signalling cascade.
The project is embedded in a group with very diverse expertise, ranging from Bioinformatics and Genomics to Plant Genetics and Biochemistry. We are looking for candidates with a solid background in molecular biology and genetics; expertise in computational data analysis and/or plant biology is a plus.
Candidates should have an advanced level in spoken and written English. If you are interested in this project, please feel free to contact Dr. Claude Becker (claude.becker@bio.lmu.de ) along with submitting your LSM application.
References:
Serra Serra, N., Schanmuganathan, R., Becker, C. (2021) Allelopathy in rice: a story on momilactones, kin recognition, and weed management. J Exp Bot, erab084, DOI: 10.1093/jxb/erab084.
Schandry, N., Becker, C. (2019) Allelopathic plants – models for studying plant-interkingdom interactions. Trends Plant Sci, 25: 176-185. DOI: 10.1016/j.tplants.2019.11.004 LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 2
For further information, please contact:
Prof. Claude Becker, claude.becker@bio.lmu.de
Reseach group website:
https://www.genetik.bio.lmu.de/research/becker/research/index.html
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Genetics
Subject areas/Research fields: Botany, Cell Biology, Genetics, Microbiology, Molecular Biology, Crop Science, Plant Protection, Mycology
Keywords: RNA biology, plant-microbe interaction, extracellular vesicles
Name of supervisor: Dr. Arne Weiberg
Project title: Pathogen extracellular vesicles in RNA effector delivery
Project description: The plant pathogens Botrytis cinerea and Hyaloperonospora arabidopsidis deliver small RNA effectors into their host plants to suppress plant immunity genes (1, 2); a process known as cross-kingdom RNAi (3). How are pathogen small RNAs transported into plant cells? Recent studies suggest that extracellular vesicles (EVs) (4), play an important role in plant cross-kingdom host-pathogen communication (5). Are EVs a means of RNA transport during plant infection?
We are seeking for a talented young career researcher, who is passionate about molecular biology and RNA science, and is willing to join our team and take together with us the next step for uncovering the fascinating, yet unknown mechanisms involved in cross-kingdom RNAi.
The research project offers to elucidate the molecular mechanisms and functions of EV-based small RNA transport from pathogens into the host plants Arabidopsis and tomato. By mass spec analysis, we identified protein candidates to be involved in small RNA transport and cross-kingdom RNA communication.
Your task will be to unravel their functions by applying modern genetical, biochemical, and cell biological methods that will pave the way for a better understanding of the RNA delivery mechanisms from pathogens into host plants and to use this knowledge to develop innovative RNAi-based crop protection strategies.
References:
1. F. Dunker, …, A. Weiberg, Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. Elife 9, e56096 (2020).
2. A. Weiberg et al., Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342, 118-123 (2013).
3. A. Weiberg, M. Wang, M. Bellinger, H. Jin, Small RNAs: a new paradigm in plant-microbe interactions. Annu Rev Phytopathol 52, 495-516 (2014).
4. A. Ruf, …, A. Weiberg, Spotlight on plant RNA-containing extracellular vesicles. Curr Opin Plant Biol 69, 102272 (2022).
5. S. Kwon, C. Tisserant, M. Tulinski, A. Weiberg, M. Feldbrügge, Inside-out: From endosomes to extracellular vesicles in fungal RNA transport. Fung Biol Rev 34, 89-99 (2019).
To find out more details, you are welcome to visit our Research group website: www.weiberglab.org For further information, please contact: Dr. Arne Weiberg, Email: a.weiberg@biologie.uni-muenchen.de
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Genetics
Subject areas/Research fields: Microbiology, Plant Science
Keywords: Xylella fastidiosa, plant immunity, chitin
Name of supervisor: Prof. Silke Robatzek
Project title: Decoding the chitin signatures generated by Xylella fastidiosa
Project description:
The ability to degrade chitin is essential for the survival and colonization success of fungal and bacterial pathogens, many of which are causal agents of agronomically-important diseases. For bacterial pathogens, which lack chitin, the degradation of chitin plays a major role in opposing host-colonizing fungi and surviving in its vector, if transmitted by insects.
One of the pathogens ranked in the “list of priority pests” for Europe is Xylella fastidiosa. This insect-transmitted bacterium is the cause of the OLIVE QUICK DECLINE SYNDROME (OQDS) and important for outbreaks over the past ten years. The urgency to develop an understanding how X. fastidiosa colonizes its hosts is apparent from the lack of disease control.
Our focus is chiA, because this proposed bacterial chitinase is secreted by X. fastidiosa and has been reported i) to confer utilization of chitin as a carbon source, potentially from its insect vectors and xylem-colonizing fungi, ii) to promote transmission by insect vectors, and iii) is required for systemic infection in plants.
Although chitinases have been studied since decades, we have little knowledge on substrate-structure-product-bioactivity relationships, which are key to understanding its role as virulence factors. Here, our goal is to answer two key questions: 1. How does X. fastidiosa degrade chitin? LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 2
2. What is the immunomodulatory potential of chitin oligomers produced by X. fastidiosa?
Being an important virulence factor, our overall aim is to better understand the molecular details of chiA function and clarify its role in systemic plant infection. We envisage that this knowledge could be useful for biotechnological purposes. The project will be funded through the DFG-funded priority program SPP2416 CodeChi https://codechi.de/
References:
(Landa et al., 2022)
Landa, B.B., Saponari, M., Feitosa-Junior, O.R., Giampetruzzi, A., Vieira, F.J.D., Mor, E., and Robatzek, S. (2022). Xylella fastidiosa’s relationships: the bacterium, the host plants, and the plant microbiome. New Phytol 234, 1598-1605.
For further information, please contact: Silke Robatzek, robatzek@bio.lmu.de
Reseach group website: https://robatzeklab.org/
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite |
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Molecular Biology
Subject areas/Research fields: botany/plant sciences, microbiology, genetics, cell biology, physiology
Keywords: acclimation, photosynthesis, cyclic electron flow, suppressor screen
Name of supervisor: Prof. Dario Leister
Project title: Acclimation to fluctuating light: cyclic electron flow
Project description:
Under natural conditions, light intensities fluctuate. Therefore, proper regulation of photosynthesis is crucial for effective plant performance under fluctuating light (FL). Cyclic electron flow (CEF) involves two thylakoid membrane proteins, PGR5 and PGRL1, both of which are critical for plant development under FL. Several lines of evidence suggest that PGR5 and PGRL1 form a complex in the thylakoid membrane.
However, the precise mechanism of their action, the regulation of their respective activities, and whether this process has the potential to enhance acclimation to FL remain elusive. In preliminary work, we have shown that PGR5 and PGRL1 can reconstitute CEF in the cyanobacterium Synechocystis sp. PCC 6803, making it possible to study PGR5-dependent CEF in a prokaryote using superior genetic tools in relatively short time spans.
We also found that the pgrl2 mutation suppresses the pgrl1 mutation, but not the pgr5 mutation – in other words: PGR5 can function without PGRL1. This result significantly revised our view of PGR5-dependent CEF, with PGR5 being the central component regulated by PGRL1 and PGRL2.
In this project, we will characterise suppressor mutations of prg5 and pgrl1 at the genetic, physiological and protein levels and set up novel suppressor screens. In addition to the model plant Arabidopsis thaliana, we will use our cyanobacterial test system with reconstructed PGR5-dependent CEF for rapid molecular and mechanistic studies. LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite |
References:
Rühle T, Dann M, Reiter B, Schünemann D, Naranjo B, Penzler JF, Kleine T, Leister D. (2021) PGRL2 triggers degradation of PGR5 in the absence of PGRL1. Nat Commun. 2021 Jun 24;12(1):3941. doi: 10.1038/s41467-021-24107-7.
For further information, please contact:
Dario Leister, leister@lmu.de
Reseach group website:
www.plantmolecularbiology.bio.lmu.de
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Keywords: endosymbiosis, dinoflagellate, adaptive laboratory evolution
Name of supervisor: Prof. Dario Leister
Project title:
Hardening corals against climate change
Project description:
Climate change is warming and acidifying the oceans, with dramatic effects including coral bleaching and impaired reef building. Several approaches have been developed to address this problem, including the hardening of the algal partner of the coral symbiosis.
Our approach is to use adaptive laboratory evolution to rapidly evolve the algal symbiont to be more resistant to relevant stresses, including high temperature and altered PH. Reintroduction of the evolved algae into the symbiotic relationship will then be tested for improved coral performance.
References:
Dann M, Ortiz EM, Thomas M, Guljamow A, Lehmann M, Schaefer H, Leister D (2021) Enhancing photosynthesis at high light levels by adaptive laboratory evolution.
Nat Plants 7: 681-695. doi: 10.1038/s41477-021-00904-2.
For further information, please contact:
Dario Leister, leister@lmu.de
Reseach group website:
www.plantmolecularbiology.bio.lmu.de
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite |
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Molecular Biology
Subject areas/Research fields: Genetics, cell biology, physiology
Keywords: chloroplast, plastid signal, GUN1, suppressor screen
Name of supervisor: Prof. Dario Leister
Project title: Regulators of chloroplast signalling
Project description:
In chloroplast signalling, the chloroplast communicates its state to the rest of the cell, in particular the nucleus, to adjust the expression of nuclear-encoded proteins targeted to the organelle. While the plastid protein GUN1 is known to play a critical role in this type of signalling in young plants, we found that GUN1 also plays a role in adult plants and in cold acclimation. In this project, we are identifying and characterising proteins that functionally interact with GUN1.
To this end, we have used genetic screens to identify a number of candidate proteins awaiting characterisation, and we are initiating novel screens. In this project, students will learn and apply techniques from genetics, molecular biology and biochemistry.
References:
Richter AS, Nägele T, Grimm B, Kaufmann K, Schroda M, Leister D, Kleine T (2023) Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. Plant Commun 4:100511. doi: 10.1016/j.xplc.2022.100511.
For further information, please contact:
Dario Leister, leister@lmu.de
Reseach group website: www.plantmolecularbiology.bio.lmu.de LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Molecular Biology
Subject areas/Research fields: Genetics, evolutionary biology, microbiology
Keywords: photosynthesis, synthetic biology, adaptive laboratory evolution
Name of supervisor: Prof. Dario Leister
Project title: Enhancing photosynthesis by synthetic biology and adaptive laboratory evolution
Project description:
In this project, parts of the light reactions of photosynthesis from very different species will be genetically combined in a model cyanobacterium. The aim is to improve photosynthesis with respect to its potential to use light of different wavelengths.
In a complementary approach, we will use adaptive laboratory evolution to make photosynthetic organisms more tolerant to different stresses, such as high light or high temperature stress. Mutations will be identified by whole genome sequencing, characterised for their molecular effects and tested for their potential to increase stress tolerance in several species.
References:
Hitchcock A, Hunter CN, Sobotka R, Komenda J, Dann M, Leister D (2022) Redesigning the photosynthetic light reactions to enhance photosynthesis – the PhotoRedesign consortium. Plant J. 109: 23-34. doi: 10.1111/tpj.15552.
For further information, please contact:
Dario Leister, leister@lmu.de
Reseach group website:
www.plantmolecularbiology.bio.lmu.de
Apply: Please send your application through the online portal of the Graduate School Life Science Munich LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 2
(LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Plant Sciences
Subject areas/Research fields: Botany, Biochemistry, Molecular Biology
Keywords: Chloroplast, Photosynthesis, Protein Biochemistry, Genomics, Imaging
Name of supervisor: Prof. Dr. Hans-Henning Kunz
Project title: Linking plastid ion transport and functionality
Project description:
All cellular organisms tightly control their inner pH and ion composition to ensure proper function of vital biochemical reactions. In eukaryotes this includes several distinct sub-cellular compartments, adding further complexity to the system. Internal homeostasis is maintained via transport proteins embedded in the organellar membranes. Our group researches the chloroplast, an organelle of endosymbiotic origin and the site of eukaryotic photosynthesis.
In the model plant Arabidopsis thaliana, we have shown that the loss of two inner envelope (IE) membrane homologous K+/H+ antiporters (AtKEA1 and AtKEA2) affects organelle biogenesis and photosynthetic performance. Our recent studies suggest defects in rRNA maturation and plastid gene expression (PGE) as the main cause for the developmental effects but the mechanistic link between the function of plastid ion transporters and the intricate gene expression machinery in the stroma remains unclear.
It is possible that the lack of AtKEA1/2 in the plastid indirectly affects nucleic acid processing and maintenance due to global effects of aberrant ion composition and stromal pH. However, IE AtKEA proteins were shown to adopt a polar distribution in young dividing or developing plastids. Interestingly, in mature organelles the protein localization seems to change again but remains limited to distinct patches within the IE. Both pattern hint at a more direct role for IE KEAs in biogenesis centers or cell/organelle cycle control.
Within these microdomain-like spots, the antiporters may tightly regulate local pH and ion concentrations necessary for proper membrane formation and organization. Intriguingly, envelope-localized KEA carriers exhibit a large N-terminal stromal loop, which is required for the specific localization pattern.
Additionally, the loop could enable IE KEA proteins to directly interact with nucleoid acids and/or other critical components of PGE. To address these questions, we have escaped the complexity of multicellular plants and instead employed a more conducive model, the unicellular green algae Chlamydomonas reinhardtii. Here, a well-established genetic tool box allows the generation of knock-down/out lines and functional tagging of proteins of interest, while our analytical methods established for plants remain applicable.
Chlamydomonas possess a haploid genome with less genetic redundancy than diploid plants. Each cell contains only one single plastid. Different from Arabidopsis, plastome transformation is relatively easy which will allow us to generate plastid expression / translation reporter lines and genetically plastome encoded ion/pH biosensors.
The cell-cycle of Chlamydomonas cultures can be synchronized and chloroplast/cell division of individuals can be closely monitored by single cell live imaging. Photosynthetic performance of single algae cells will be probed by microscopy Pulse Amplitude Modulation (PAM). Elemental composition of genotypes will be analyzed by Total Reflection X-ray Fluorescence Spectroscopy (TXRF). In parallel, we aim on dissecting protein function by obtaining biochemical and structural information from in-vitro approaches. The homolog of KEA1/2 in LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 2
Chlamydomonas will be the starting point for our study before focusing on the functional characterization of other plastid localized carriers.
We seek to train a highly motivated PhD student on this project. The ideal candidate would have basic experience in plant and/or algae molecular biology and a solid background in biochemistry and cell biology.
References:
DeTar RA, Barahimipour R, Manavski N, Schwenkert S, Höhner R, Bölter B, Inaba T, Meurer J, Zoschke R, Kunz HH. Loss of inner-envelope K+/H+ exchangers impairs plastid rRNA maturation and gene expression. Plant Cell. 2021 Aug 13;33(7):2479-2505. doi: 10.1093/plcell/koab123. Erratum in: Plant Cell. 2021 Sep 18;: PMID: 34235544; PMCID: PMC8364240.
Aranda-Sicilia MN, Aboukila A, Armbruster U, Cagnac O, Schumann T, Kunz HH, Jahns P, Rodríguez-Rosales MP, Sze H, Venema K. Envelope K+/H+ Antiporters AtKEA1 and AtKEA2 Function in Plastid Development. Plant Physiol. 2016 Sep;172(1):441-9. doi: 10.1104/pp.16.00995. Epub 2016 Jul 21. PMID: 27443603; PMCID: PMC5074627.
Schroda M, Remacle C. Molecular Advancements Establishing Chlamydomonas as a Host for Biotechnological Exploitation. Front Plant Sci. 2022 Jun 29;13:911483. doi: 10.3389/fpls.2022.911483. PMID: 35845675; PMCID: PMC9277225.
For further information, please contact:
Prof. Hans-Henning Kunz, kunz@lmu.de
Research group website:
https://www.en.botanik.bio.lmu.de/research/kunz/research/index.html
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM). LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 1
Open position for the LSM call of applications
Department/Institute: LMU Faculty of Biology, Genetics
Subject areas/Research fields: Plant Sciences, Genetics, Molecular Biology, Computational Biology
Keywords: epigenetics; epigenomics; DNA methylation; plant microbiome
Name of supervisor: Prof. Dr. Claude Becker
Project title: Epigenomic associations with plant-microbe interactions
Project description: Plants grow in a diverse community with microorganismic interactors, which range from pathogens to beneficial symbionts. In recent years, it has become apparent that the plant epigenome, the combination of chemical modifications to DNA and histones, plays a role in modulating both pathogenic and symbiotic interactions (reviewed in Ramos Cruz et al., Curr Opin Plant Biol 2021).
In this project, we want to identify which epigenomic loci are associated with the overall plant microbiome profile. Using a set of well-characterized Arabidopsis thaliana lines that have mosaic DNA methylation patterns, we will profile the overall root and leaf microbiome of these plants when grown in the same soil using metagenome sequencing via 16S rRNA and ITS profiling.
We will then map microbial diversity and relative abundance to the epigenomic variation and combine these analyses with de novo generated transcriptome profiles. Our goal is to identify loci that are subject to epigenetic regulation and that modulate the overall interaction with microbial organisms. In a second phase, we will transition from the A. thaliana model to crop plants.
The project is embedded in a group with very diverse expertise, ranging from Bioinformatics and Genomics to Plant Genetics and Molecular Biology. We are looking for candidates with a solid background in molecular biology and genetics; expertise in computational data analysis and/or plant biology is a plus. Candidates should have an advanced level in spoken and written English. If you are interested in this project, please feel free to contact Dr. Claude Becker (claude.becker@bio.lmu.de ) along with submitting your LSM application.
References:
Ramos-Cruz, D., Troyee, D., Becker, C. (2021) Epigenetics in plant organismic interactions. Curr Opin Plant Biol, 61: 102060. DOI: 10.1016/j.pbi.2021.102060
Wibowo, A.*, Becker, C.*, Durr, J., Price, J., Spaepen, S., Hilton, S., Putra, H., Papareddy, R., Saintain, Q., Harvey, S., Bending, G.D., Schulze-Lefert, P., Weigel, D., Gutierrez-Marcos, J. (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. PNAS, 115: E9145-9152. https://doi.org/10.1073/pnas.1805371115 LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN Seite | 2
For further information, please contact:
Prof. Claude Becker, claude.becker@bio.lmu.de
Reseach group website:
https://www.genetik.bio.lmu.de/research/becker/research/index.html
Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM).