Unravelling the RNA binding proteome of Synechocystis sp. PCC6803

Abstract: Cyanobacteria are among the oldest life forms on Earth, with their presence confirmed through microfossils. They played a fundamental role in the Great Oxygenation Event billions of years ago by developing oxygenic photosynthesis. Thriving in a wide range of environments where light is present, cyanobacteria encounter fluctuating conditions such as nutrient availability, temperature variations, and changing light intensities. To adapt to these challenges, cyanobacteria have evolved a range of regulatory mechanisms, including sophisticated RNA-based regulation.
Regulatory RNA molecules, particularly small noncoding RNAs (sRNAs), play a crucial role in bacterial gene expression. sRNAs often modulate the translation of target mRNAs through complementary base pairing. In the cyanobacterium Synechocystis sp. PCC 6803, sRNAs regulate key pathways, including iron homeostasis, photosynthesis, mixotrophic growth, and nitrogen metabolism. Additionally, mRNA localization within the cell significantly influences protein expression and function. Both RNA-based regulation and mRNA localization depend on RNA binding proteins (RBPs), which govern processes ranging from transcription termination/ antitermination and translation initiation or delay to RNA decay. While well-studied in bacteria like Escherichia coli and Salmonella, RBP candidates and functions in cyanobacteria remain largely unexplored. Recently potential RBPs in Synechocystis sp. PCC 6803 were identified via GradSeq, but their roles require further validation. Notably, a family of cyanobacterial proteins harboring the RNA recognition motif (RRM) appears to transport photosystem-related mRNAs to the thylakoid membrane.
In this study, we demonstrate the interaction between the YlxR protein, identified in the GradSeq analysis, and RNase P, highlighting the importance of RBPs in RNA processing pathways such as tRNA maturation. Additionally, we establish that Rbp3, a conserved cyanobacterial protein with an RRM, is crucial for maintaining photosystem I levels. Our research identifies several Rbp3 interaction partners, predominantly membrane-associated proteins or those in close proximity to membranes and carboxysome proteins. We also reveal the association of Rbp3 with ribosomes and factors potentially involved in RNA stability and translational control, suggesting roles beyond transcript localization. Furthermore, we aided by elucidating the fine-tuning mechanism of an sRNA involved in the regulation of nitrogen metabolism, providing insights into the complexity of sRNA-mediated regulatory networks. Moreover, we sought to discover novel RBPs using an RNase-sensitive gradient approach. We developed an analytical tool based on the Jensen-Shannon distance and replicate similarity for dataset analysis and visualization. This method identified several new RBP candidates.
In summary, this work underscores the significance of RBPs in essential processes such as tRNA maturation, transcript localization and identifies additional potential RBPs in Synechocystis sp. PCC 6803

Angaben zum Objekt

• Standort: Deutsche Nationalbibliothek Frankfurt am Main
• Umfang: Online-Ressource
• Sprache: Englisch
• Anmerkungen: Universität Freiburg, Dissertation, 2024

Klassifikation und Themen

• Schlagwort: RNS ; Synechocystis ; Proteomanalyse ; Strukturaufklärung ; Cyanobakterien

Beteiligte, Orts- und Zeitangaben

• Ereignis: Veröffentlichung
• (wo): Freiburg
• (wer): Universität
• (wann): 2024
• Urheber: Hemm, Luisa
• Beteiligte Personen und Organisationen: Hess, Wolfgang ; Wilde, Annegret ; Albers, Sonja Verena ; Albert-Ludwigs-Universität Freiburg. Institut für Biologie III ; Albert-Ludwigs-Universität Freiburg. Fakultät für Biologie

Weitere Informationen

• DOI: 10.6094/UNIFR/258984
• URN: urn:nbn:de:bsz:25-freidok-2589846
• Rechteinformation: Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
• Letzte Aktualisierung: 15.08.2025, 07:25 MESZ