It is widely accepted that the energy-producing organelles of eukaryotic cells, mitochondria and chloroplasts, are derived from once free-living ancestors. In the course of evolution, the vast majority of genes have been relocated to the nucleus. If the function of the proteins encoded by these genes is still important in today’s world, they are imported into the organelles after being translated on cytosolic (eukaryotic) ribosomes. But, why are some genes kept in the miniature genomes of mitochondria and chloroplasts? It has been proposed that genes are retained in organelles because their codon usage or base composition might prevent the efficient expression of organellar genes in the nucleus, because some proteins might be difficult to import across the double organelle membranes, or because their expression must be tightly coupled to the redox state of the respective electron transport chains.
In our Opinion paper in Trends in Plant Science (2025), we propose that mRNA targeting is a previously unappreciated mechanism to explain gene retention in chloroplasts. In brief, we propose that mRNAs encoding proteins central to photosynthesis have to interact with the thylakoid membrane systems and that this is critical for localizing the encoded proteins to the membrane, and coordinating early steps of complex assembly.
We developed this idea, based on recent experimental data, together with Conrad Mullineaux (London) and Annegret Wilde (Freiburg).

There are hundreds of small genes of unknown function in bacterial genomes. In our recent study in Current Biology 32, 136-148 (Song et al., 2022a) we have characterized the function of one of them, atpT. This gene encodes the only 48 amino acid protein AtpΘ, which we characterized as a small protein inhibitor of the ATP synthase. Under unfavorable conditions, AtpΘ is expressed and inhibits the reverse reaction of ATP synthase, which burns ATP to transport protons across the membrane. AtpΘ is conserved in cyanobacteria and its function is related to the unique fact that the ATP synthase in cyanobacteria is ultimately driven by the photosynthetic and the respiratory electron transport chains, both located within the same thylakoid membrane system. The gene atpT was first identified in Synechocystis sp. PCC 6803 as norf1 (Mitschke 2011) and later recognized as the single most-strongly induced protein-coding gene when cyanobacteria encounter darkness (Kopf et al., 2014; Baumgartner et al., 2016). We further found that this up-regulation is closely linked to the energy and redox status of the cell, which is largely mediated by changing the stability of the atpT mRNA (Song et al., 2022b) and developed a protocol for the preparation of intact and active FoF1 ATP synthase (Song et al., 2022c).  

Congratulation to Kuo to make this story the topic of his successful PhD thesis! Special thanks go to Sandra Maaß and Dörte Becher from the Department of Microbial Proteomics at the University of Greifswald, to Martin Hagemann from the University of Rostock and to Alicia Muro-Pastor from the Instituto de Bioquimica Vegetal y Fotosintesis, CSIC and the Universidad de Sevilla, Spain, for the great collaboration. We thank the China Scholarship Council for funding Kuo Song through a scholarship grant and the Deutsche Forschungsgemeinschaft for support through the priority program SPP 2002 “Small Proteins in Prokaryotes, an Unexplored World” and the RTG MeInBio - 322977937/GRK2344. Thanks also to Robert Burnap for writing this article on “Bioenergetics: To the dark side and back with cyanobacterial ATP synthase” as a comment on our paper.

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.

Matthias has defended his doctoral thesis on "The complexity of gene regulatory networks in a photosynthetic model organism" at October 26, 2020, with summa cum laude. Big congratulations to this outstanding result and thanks to the DFG for funding through the “MeInBio – BioInMe” PhD program!

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".