Global discovery of RNA modifications and functional analysis of m⁵C methylome in cyanobacteria

RNA modifications have been found in all domains of life and play regulatory roles in diverse biological processes. However, their distribution, function, and regulation in cyanobacteria remain unexplored. Here, we have employed a quantitative RNA profiling strategy based on mass spectrometry analysis to identify 21 different RNA modifications in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Mass spectrometry analyses reveal a dynamic pattern of these RNA modifications under different culture conditions. We subsequently perform transcriptome-wide 5-methylcytosine (m⁵C) profiling in Synechocystis by using bisulfite sequencing. In total, we identify 824 high-confidence m⁵C sites in 382 mRNAs, with the majority of m⁵C-modified genes participating in ribosome, RNA degradation, carbon metabolism, and photosynthesis. Combined with the m⁵C-RNA immunoprecipitation detection method, 40.17% (331) m⁵C sites were validated and located within 129 m⁵C-RNA immunoprecipitation peaks on 145 mRNAs. Notably, integrated transcriptomic, proteomic, and m⁵C methylome analysis shows that m⁵C modification is negatively associated with protein abundance and contributes to the RNA-protein discordance, implying the importance of m⁵C on post-transcriptional regulation in Synechocystis. Collectively, our study provides a holistic view of RNA modifications and the first mRNA m⁵C map in cyanobacteria, which present a critical database for functional analyses of RNA modifications in cyanobacteria. The method used in this study is applicable to any sequenced prokaryotes and could be applied as a standard part of transcriptomic analysis.