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.