Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria

Bacterial genomes are not only densely packed for the ‘normal’ protein-coding genes but harbor also hundreds of genes for non-coding RNAs and an unknown number of small genes encoding peptides and small proteins. In functional analyses, these small genes are often overlooked.
NsiR6 was initially identified in Synechocystis sp. PCC 6803 as a transcript induced by nitrogen starvation (Kopf et al., 2014). We then showed that it is not a regulatory (non-coding) sRNA but encodes a small protein of 66 amino acids (Baumgartner et al., 2016). Looking for its possible function, we have now characterized it as a phycobilisome break-down factor during nitrogen starvation.
Phycobilisomes are very efficient light-harvesting structures but they are costly to make because their synthesis require substantial amounts of organic nitrogen. To recycle this nitrogen, cells disassemble phycobilisomes during periods of nitrogen starvation, leading to severe loss in pigmentation, which is visible to the naked eye as chlorosis or bleaching. We found that lack of the nsiR6 gene in deletion mutants led to a non-bleaching phenotype, therefore we renamed the nsiR6 gene to nblD. Homologs of nblD are widely conserved in phycobilisome-containing cyanobacteria.
The encoded protein, NblD, binds in a very specific way to the phycocyanin beta subunit (CpcB), but only when the CpcB protein has chromophores bound. This points to a special role in dealing with the light-absorbing pigment-protein complexes, which are potentially dangerous for the cell during phycobilisome disassembly. To gain insight into the function of NblD, extensive pull-down assays and mass spectrometry analyses and Far Western blot have proven crucial.
Please read the full story here: Krauspe et al. (2021). A short comment in German can be found here.

Special thanks go to Matthias and Oliver at the Medical Center of our university, to Philip and Boris at the Department of Quantitative Proteomics at the University of Tübingen and to Nicole at the University of Kaiserslautern for the great collaboration. We thank our colleagues for helpful discussions and the Deutsche Forschungsgemeinschaft for funding Vanessa through the priority program SPP 2002 “Small Proteins in Prokaryotes, an Unexplored World”, facilitating collaboration within the research group FOR2816 “SCyCode” and through the RTG MeInBio – 322977937/GRK2344.

The messenger between: How mRNAs convey genetic information to the sites of photosynthetic complex assembly

Photosynthesis is the biological process in which solar energy is converted into chemical energy. The energy is then used to produce organic molecules from carbon dioxide. The key reactions of photosynthesis occur in plants, algae and cyanobacteria in two complex structures, the photosystems. While it is well known that the functional photosystems reside in a special membrane system, the thylakoids, many details of their molecular assembly and the insertion of the proteins into the membranes have remained unknown. A surprising discovery now published in Nature Plants (07 September 2020) demonstrates that it is not the pre-synthesized protein that is transported to the thylakoid membranes for photosystem assembly. Instead, the mRNAs encoding core proteins of the photosystems are transported to the thylakoid membranes in a ribosome-independent process. The findings contribute to a developing concept that mRNA molecules can provide much more than just the sequence of the protein: in this case they also carry signals that seem to control the location and co-ordination of photosystem assembly. The identification of two proteins likely involved in this process by interacting with these mRNAs opens the road towards the detailed understanding of the molecular mechanisms involved. These results have been obtained in an international cooperation between Cyanolab (special congratulations to Luisa and Matze!), Annegret Wilde (Bacterial Genetics Freiburg), Satoru Watanabe (Tokyo, Japan) and was led by the former FRIAS fellow Conrad Mullineaux (Queen Mary University of London, UK). We are grateful for support by the DFG-funded Graduate School 2344 “MeInBio – BioInMe: Exploration of spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods“. 

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.