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

RNA Biol. 2014;11(7):855-64. doi: 10.4161/rna.29440. Epub 2014 Jun 12.

Abstract

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.

Keywords: RNA decay; RNase J; ribosome degradation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism*
  • Molecular Sequence Data
  • Mutation
  • RNA Stability
  • RNA, Bacterial / metabolism
  • RNA, Messenger / metabolism*
  • Rhodobacter sphaeroides / enzymology*
  • Rhodobacter sphaeroides / genetics
  • Sequence Analysis, RNA

Substances

  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Messenger
  • Exoribonucleases

Associated data

  • GEO/GSE54750