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.
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.
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.
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!
Cyanolab is located at the interface of bioinformatics, experimental RNA biology and microbial systems biology. 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 Hess et al., 2014; Georg 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; Voigt et al., 2014; Walworth et al., 2015).
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 (Georg et al., 2009; Voß et al., 2009; Wright et al., 2013, 2014). We study CRISPR systems with the aim to understand their functions in antiviral defense and also beyond defense (see, for instance, the publications Hein et al., 2013; Scholz et al., 2013).
Particular research has been applied on marine microoganisms and the marine microbiome (Voss et al., 2013; Kopf et al., 2015). 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).
Dr. Matthias Kopf (Matze) has been awarded the Hans-Grisebach price for his outstanding summa cum laude dissertation in the field of comparative transcriptomics! Congratulations!!