Cyanolab, the Genetics and Experimental Bioinformatics unit at the University of Freiburg, Germany, is searching for a scientist to participate in the DFG-funded Priority Program SPP 2141 “Much more than Defence: The Multiple Functions and Facets of CRISPR-Cas” within the project "Cross-talk and extensive rewiring of CRISPR-Cas systems with the cellular regulatory machinery in Cyanobacteria". The intended start date is within the last three months of 2018 or early in 2019, or upon negotiation and the position is limited to a duration of 3 years.
For recent relevant publications of our laboratory, see Nature Microbiology 3, 367–377; Trends in Biotechnology 36, 996-1010; Cell Reports (2018) 22, 3377–3384; PLoS ONE (2013), 8(2), e56470.
The project tasks will include the analysis of RNA-protein interactions that have an impact on the prokaryotic immune system, with a focus on the cyanobacterial model organism Synechocystis. The work plan includes the immunoprecipitation, isolation and characterization of ribonucleoprotein complexes, the analysis of transcriptomic datasets and transcription factor binding motifs, the generation and molecular analysis of cyanobacterial mutant strains and the study of intracellular interactions with invader DNA and bacteriophages.
For this we seek a highly motivated candidate with a background in biochemistry, molecular biology or molecular genetics (M.Sc. or diploma level).
The project aims at a fundamental understanding of the interactions between the prokaryotic CRISPR-Cas system and the host cell’s regulatory mechanisms. The work is carried out within an ongoing international collaboration and as part of DFG-funded consortium that involves regular meetings and timely delivery of results. 

Cyanolab is located at the University of Freiburg, located in one of the most beautiful regions of Southern Germany in the heart of Europe. Freiburg is known for its high quality of life at the slopes of the Black Forest, close to the Alps, Switzerland and France. The Faculty of Biology at the University of Freiburg is one of the leading Life Science Departments in the country.

Please send your application by Email to: wolfgang.hess@biologie.uni-freiburg.de
In your application, please include (1) a CV in tabular form, (2) a brief summary of previous research experience and academic qualification, (3) scanned copies of university degrees and (4) contact details for at least one reference.

Transcription factors of the GntR type possess two domains: a DNA binding domain in the N-terminal part, and a putative ligand-binding domain in the C-terminal section. Upon ligand binding, the protein activity is modified, leading to a change in the regulation of gene expression. Therefore, GntR-type transcriptional regulators are prime candidates to synchronize metabolism and transcription, especially in Cyanobacteria with their versatile pathways for photosynthesis-driven carbon and nitrogen assimilation. With their new paper “The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria” the cyanolabbers Joke, Mascha and Claudia provide for the first time insight into the activity of such a transcription factor from the marine cyanobacterium Prochlorococcus MED4.  

Shengwei has defended his doctoral thesis on „Genomic and Transcriptomic Analyses of Marine Microorganisms“ at April 09, 2018. Big congratulations and we wish you success and a good start in the new lab at UCLA!

In our paper "The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a CRISPR–Cas subtype III-Bv system" we show that RNase E is the maturation endoribonuclease of a variant CRISPR system. For the details, please see the publication in Nature Microbiology 3, 367–377 (2018). Please see also our press release. Funding for this research came from the German Research Foundation as part of a grant for the FOR1680 research group: "Unravelling the Prokaryotic Immune System CRISPR-Cas" and the Freiburg Institute for Advanced Studies.

In a joint publication with Shoshy Altuvia’s lab at the Hebrew University of Jerusalem we have studied how the small RNA OxyS protects bacterial cells from DNA damage – see our new paper in The EMBO Journal (2018) 37: 413–426 “OxyS small RNA induces cell cycle arrest to allow DNA damage repair”. This work was supported by a grant from GIF.

The topic of epigenetics in Cyanobacteria was tackled in our work “Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803”, which has appeared in DNA Research. Especially interesting is that the lack of N4-cytosine methylation affects growth and pigmentation of this unicellular cyanobacterium. This work resulted from our long-standing collaboration with the lab of Martin Hagemann at the University of Rostock and the Max Planck-Genome Center Cologne.

Further studying the model cyanobacterium Synechocystis sp. PCC 6803, we contributed to the identification of a previously unknown regulatory set of genes putatively involved in the process of recovery from iron limitation. This work, which resulted from collaboration with Nir Keren's group at the Hebrew University in Jerusalem, has appeared in The Plant Journal (2018) 93: 235-245.

Asking the question "How can microbes prioritize their responses to multiple environmental stresses?" we found that the sRNA IsaR1 is involved in integrating the responses to iron limitation and high salinity - see our new paper in Environmental Microbiology: "The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp. PCC 6803".  IsaR1 is an only 68 nt regulatory sRNA that mainly controls the acclimation of oxygenic photosynthesis to iron starvation, details here. This work resulted from our collaboration with the Plant Physiology lab at the University of Rostock and the "Applied Metabolome Analysis" group at the MPI in Golm. Stephan, who has been leading this project is now at the Centre for Environmental Research. Congratulations!

Marine bacteria and Cyanobacteria were studied in another 3 publications. In “Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise” we investigated how a marine copiotroph benefits from photosynthesis in the co-occurring Trichodesmium. For the details, see our full paper in ISME J. presenting the results of a great collaboration between 4 labs in Germany, Israel and Spain.

In a another great collaboration, with Kaarina Sivonen’s lab in Helsinki, we have investigated Nodularia spumigena, a nitrogen-fixing cyanobacterium that forms toxic blooms in the Baltic Sea each summer. The results from this work are presented in two papers, which appeared in The ISME Journal and in Frontiers in Microbiology. Of special interest are the findings that these bloom-forming cyanobacteria degrade methylphosphonate and release methane.

This month our paper "Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1" has been published in the latest issue of Current Biology. IsaR1 is a regulatory RNA molecule that controls the acclimation of cells and especially of the photosynthetic machinery to limiting concentrations of bio-available iron. Please see also our press release and this comment. This work has been a productive collaboration among laboratories in 5 different countries.