GntR-type transcription factor PMM1637 from Prochlorococcus MED4

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.  

Congratulations to Shengwei!

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 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.

Cyanolab publications in September/October 2016

In September and October 2016 Cyanolab contributed to five publications.

Research on CRISPR RNA endonucleases: In our article „Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs“ in Nucleic Acids Research we investigated two CRISPR-associated RNA endonucleases of the Cas6 family. Small RNA molecules generated by the activity of Cas6 enzymes are an essential element of all CRISPR-Cas systems in the recognition of invading phage DNA or other nucleic acids. However, many bacteria and archaea possess multiple systems and several Cas6 endonucleases. It is poorly understood what makes these enzymes able to keep their substrates apart from each other. We found that the enzymes Cas6-1 (Slr7014) and Cas6-2a (Slr7068) can, despite their sequence identity of only 16.5 %, recognize the respective non-cognate substrate in vitro but not in vivo. We further found that adjacent spacer sequences can interfere with the formation of the short hairpin element within the substrate RNA that is required for proper recognition. This work was supported by the German Research Foundation (DFG) program FOR1680 “Unravelling the Prokaryotic Immune System” and is a joint publication with the group of Rolf Backofen.

Two articles dealt with the regulation of gene expression in cyanobacteria: In “Awakening of a dormant cyanobacterium from nitrogen chlorosis reveals a genetically determined program” in Current Biology the genetic program is described that governs the awakening of a dormant bacterium from nitrogen chlorosis back to photosynthetically active life. This work was performed in collaboration with partners in Germany, the Czech Republic and Japan, led by Karl Forchhammer at the Institute of Microbiology at the University of Tübingen. The results have wide-ranging implications for the understanding of bacterial persistence and cellular aging. More information can be found also here.
In “CyAbrB2 contributes to the transcriptional regulation of low CO2 acclimation in Synechocystis sp. PCC 6803”, which appeared in Plant and Cell Physiology we studied the function of the transcriptional factor cyAbrB2 in the adjustment of primary carbon and nitrogen metabolism to photosynthetic activity under fluctuating environmental conditions.

Two publications targeted the adaptation of microorganisms to the marine environment: In “Trimethylated homoserine functions as the major compatible solute in the globally significant oceanic cyanobacterium Trichodesmium” in PNAS the chemical compound was identified and the biosynthetic pathway leading to it elucidated that assures robust survival under the osmotically harsh high salinity within the marine environment. Globally, substantial amounts of organic carbon are stored in this compound, homoserine betaine, as it contains three methyl groups and occurs in high intracellular concentrations. Thus, its sudden release during the demise of high-density surface blooms of Trichodesmium will impact the marine microbial community. This work was performed in collaboration with partners in Germany and Israel and was led by Martin Hagemann at the Life Sciences Institute of the University of Rostock. More (in German) can be found also here.

In our article „mdRNAseq analysis of marine microbial communities from the northern Red Sea”, which was published in Scientific Reports, we have employed Differential RNA-Seq to analyze the primary transcriptomes of a complex marine microbiome sample. This technique, not previously used for metatranscriptomics, is powerful for the simultaneous identification of transcriptional start sites (i.e., the suite of active promoters) and the analysis of gene expression at community-wide scale. We identified promoters active in situ for five different pico-planktonic organisms genera belonging to the three domains of life (the SAR11 clade of Alphaproteobacteria, Synechococcus cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities.

Cyanolab publications in July 2016

In July 2016 four publications have appeared to which Cyanolab has contributed.

New regulatory RNA: In the publication de Porcellinis et al. (2016) we characterize PmgR1, a small RNA that is involved in the regulation of growth under photomixotrophic conditions and glycogen metabolism.

Mechanisms for self-destruction: In Kopfmann et al. (2016) we present an overview on the type II toxin-antitoxin systems in the cyanobacterial model Synechocystis sp. PCC 6803. This organism possesses with 69 type II toxin-antitoxin systems plus seven stand-alone components a startling number of such systems. These systems are dangerous biological entitities: Activation of the toxin may lead to the self-destruction of the cell. Indeed, some of these systems function in the post-segregational killing of cells that have lost the plasmid encoding it. However, for the vast majority of toxin-antitoxin systems the functions have remained unknown, especially when encoded in the chromosome. The comprehensive list of these systems will be helpful in their further functional analysis.

Metatranscriptomic analysis of the near-surface microbiome in the South-West Pacific: Two studies contribute to the deeper understanding of marine microbial communities. The work by Pfreundt et al. (2016a) presents the metatranscriptomic analysis of microbial activities within a large mesocosm and the surrounding lagoon waters in the South-West Pacific, 35 km off the coast near Noumea, New Caledonia, over a time of 23 days. In the study by Spungin et al. (2016), cells of the important nitrogen fixer Trichodesmium were collected and studied during the crash of a bloom-like population. Metatranscriptomic profiling showed the  upregulated expression of several putative metacaspase genes, suggesting their involvement in the termination of the dense agglomerations of Trichodesmium. These two papers result from our participation in the VAHINE project.

Congratulations to Ulrike

On July 28 Ulrike (Uli) Pfreundt has defended her doctoral thesis on „The non-coding paradox of Trichodesmium – Lifestyles and strategies in the oligotrophic marine environment“ with the highest possible rating summa cum laude. Big congratulations to this phantastic outcome!

What we do

Cyanolab is located at the interface of bioinformatics, synthetic biology, 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 Research Group FOR 2816 “The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers (SCyCode)” the DFG Priority Programs SPP 2002 “Small Proteins in Prokaryotes, an Unexplored World“,  SPP 2141 “Much more than Defence: the Multiple Functions and Facets of CRISPR-Cas“, SPP 2237 „MAdLand – Molecular Adaptation to Land: plant evolution to change“ and SPP 2389 „Emergent Functions of Bacterial Multicellularity“.

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; Riediger et al., 2019 and 2021; Rübsam et al., 2018; 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., 2018a and 2018b; Hein et al., 2013; Kieper et al., 2018; Mitrofanov et al., 2022; Reimann et al., 2017 and 2020; Scholz et al., 2013; Shah et al., 2018; Ziemann et al., 2023).

On the basis of comparative genomic information, computational and experimental tools have been developed and applied to systematically investigate the „genetic dark matter“. This includes the identification of  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; Georg and Hess, 2018; Lott et al., 2018; Voß et al., 2009; Wright et al., 2013 and 2014; Zhan et al., 2021; Zhang et al., 2022). Further in this field, we have discovered two small proteins, which function as novel players in the regulation of the primary energy metabolism (Krauspe et al., 2021; Song et al. 2022). 

Particular research has been conducted on marine microorganisms and the marine microbiome (Hou et al., 2018; Lott et al., 2020; Teikari et al., 2018a, 2018b; Voigt et al., 2014). In the characterization of the marine microbiome we have been studying the microbial metatranscriptome and community composition (Pfreundt et al., 2016a,b; Spungin et al., 2016; van Wambeke, 2016).