Characterization of YlxR/Ssr1238, a conserved RNA binding protein in a model cyanobacterium

We characterized the predicted RNA-binding protein Ssr1238 from the model cyanobacterium Synechocystis sp. PCC 6803. Co-immunoprecipitation of proteins followed by MS analysis and sequencing of UV-cross-linked co-immunoprecipitated RNA samples identified potential interaction partners of Ssr1238. The most highly enriched transcript was the RNase P RNA, while RnpA, the protein component of RNase P was among the most highly enriched proteins, consistent with recent findings that YlxR proteins can influence the enzymatic activity of RNase P. A second highly enriched transcript derived from the 3prime region of gene ssl3177, which encodes a rare lipoprotein homolog, a central enzyme in cell wall remodeling during cell division. The data also show a strong connection to the RNA maturation and modification system indicated by co-precipitation of riboendonuclease E, RNA methyltransferase Sll1967, the A-adding tRNA nucleotidyltransferase Sll1253 and queuine tRNA-ribosyltransferase, as well as enolase. Thus, Ssr1238 specifically binds two different transcripts and appears to participate in the coordination of RNA maturation, translation and cell division. Our results are consistent with recent findings that the B. subtilis YlxR protein functions as an RNase P modulator (RnpM), extend its proposed role to the phylum cyanobacteria and suggest additional functionalities.