In the first 8 weeks of 2018, Cyanolab has contributed to eight publications

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.

Cyanolab in May 2017 “Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1”

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.

What we do

Cyanolab is located at the interface of bioinformatics, experimental RNA biology and microbial systems biology. We participate in the Research Training Group “MeInBio – BioInMe: Exploration of spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods“, the DFG Priority Program SPP 2002 “Small Proteins in Prokaryotes, an Unexplored World” and the DFG Research Group FOR 1680 “Unravelling the prokaryotic immune system CRISPR-Cas“.

We have a long-standing interest in cyanobacteria and other photosynthetic organisms and their functions in the environment and their biotechnology. Current research activities are centered around the analysis of transcriptomic and epigenomic datasets to characterize regulatory RNAs and epigenetic modifications (see, for instance, our publications Hagemann et al., 2018; Hess et al., 2014; Klähn et al., 2015; Kopf et al., 2014; Kopf and Hess, 2015; Lott et al., 2015; Mitschke et al., 2011; Pfreundt et al., 2015; Rübsam et al., 2018; Voigt et al., 2014; Walworth et al., 2015).

We study CRISPR systems with the aim to understand their functions in antiviral defense and also beyond defense (see, for instance, the publications Behler et al., 2018; Hein et al., 2013; Kieper et al., 2018; Scholz et al., 2013).

On the basis of comparative genomic information, computational and experimental tools have been developed and applied to systematically identify novel regulatory RNAs (antisense and non-coding RNAs) in diverse pro- and eukaryotic organisms and to understand their functions (Barshishat et al., 2018; Georg et al., 2009, 2014 and 2017; Lott et al., 2018; Voß et al., 2009; Wright et al., 2013 and 2014).

Particular research has been applied on marine microorganisms and the marine microbiome (Hou et al., 2018; Kopf et al., 2015; Teikari et al., 2018a, b; Voss et al., 2013). In the characterization of the marine microbiome we have contributed to the VAHINE project by studying the microbial metatranscriptome and community omposition in the South-West Pacific (Pfreundt et al., 2016a,b; Spungin et al., 2016; van Wambeke, 2016).