RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides

All bacteria contain multiple exoribonucleases to ensure a fast breakdown of different RNA molecules, either for maturation or for complete degradation to the level of mononucleotides. This efficient RNA degradation plays pivotal roles in the post-transcriptional gene regulation, in RNA processing and maturation as well as in RNA quality control mechanisms and global adaption to stress conditions. Besides different 3′-to-5′ exoribonucleases mostly with overlapping functions in vivo many bacteria additionally possess the 5′-to-3′ exoribonuclease, RNase J, to date the only known bacterial ribonuclease with this activity. An RNA-seq approach was applied to identify specific targets of RNase J in the α-proteobacterium Rhodobacter sphaeroides. Only few transcripts were strongly affected by the lack of RNase J implying that its function is mostly required for specific processing/degradation steps in this bacterium. The accumulation of diverse RNA fragments in the RNase J deletion mutant points to RNA features that apparently cannot be targeted by the conventional 3′-exoribonucleases in Gram-negative bacteria.