RNase R

RNase R, or Ribonuclease R, is a 3'-->5' exoribonuclease, which belongs to the RNase II superfamily, a group of enzymes that hydrolyze RNA in the 3' - 5' direction. RNase R has been shown to be involved in selective mRNA degradation, particularly of non stop mRNAs in bacteria.[1][2] RNase R has homologues in many other organisms.

When a part of another larger protein has a domain that is very similar to RNase R, this is called an RNase R domain.

Role in trans-translation and ribosomal quality control

RNase R ensures translation accuracy, correct rRNA maturation and elimination of abnormal rRNAs, and is employed by the trans-translation system to break down damaged mRNAs.[3]

In Escherichia coli, RNase R is a 92 kD protein, with the characteristic capacity to degrade structured RNA substrates without displaying sequence specificity. Therefore, RNase R acts over a range of substrates, such as, ribosomal, transfer, messenger and small non-coding RNAs. RNase R is associated with ribonucleoprotein complex that contains tmRNA and SmpB, and is involved in the development of tmRNA under cold-shock.[3]

RNase R is also associated with ribosomes and participates in rRNA, or ribosomal RNA, quality control processes. RNase R has an in vitro affinity for rRNA. In several rRNA quality control pathways, RNase R behaves as a mainfactor by enhancing the removal of faulty rRNA molecules. This protein is also critical for handling rRNA precursors and for observing the ribosome integrity.[3]

RNA digestion

RNase R has two cold shock domains, an RNase catalytic domain, an S1 domain and a basic domain.[4]

Overabundance of RNase R in a cell are harmful since RNase R is more active and more effective in breaking down RNAs than the other bacterial exoribonucleases, such as RNase II.[5] Besides the substrate RNAs that construct double-stranded RNA with 3' overhangs shorter than seven nucleotides, RNase R can degrade all linear RNAs.[6] For the methodical digestion of eukaryotic linear RNAs, RNase R is a good 3' to 5' exoribonuclease but there are infrequent cases of RNase R resistance. Since mRNAs are not chemically protected at their 3' ends, unlike the protection provided at their 5' ends by the cap structure, RNase R successfully degrades linear mRNAs from their unprotected 3' ends.[4]

References
  1. Cheng ZF, Deutscher MP (January 2005). "An important role for RNase R in mRNA decay". Molecular Cell. 17 (2): 313–8. doi:10.1016/j.molcel.2004.11.048. PMID 15664199.
  2. Venkataraman K, Guja KE, Garcia-Diaz M, Karzai AW (2014). "Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue". Frontiers in Microbiology. 5: 93. doi:10.3389/fmicb.2014.00093. PMC 3949413. PMID 24653719.
  3. Domingues S, Moreira RN, Andrade JM, Dos Santos RF, Bárria C, Viegas SC, Arraiano CM (July 2015). "The role of RNase R in trans-translation and ribosomal quality control". Biochimie. 114: 113–8. doi:10.1016/j.biochi.2014.12.012. PMID 25542646.
  4. Suzuki H, Tsukahara T (May 2014). "A view of pre-mRNA splicing from RNase R resistant RNAs". International Journal of Molecular Sciences. 15 (6): 9331–42. doi:10.3390/ijms15069331. PMC 4100097. PMID 24865493.
  5. Cheng ZF, Deutscher MP (June 2002). "Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II". The Journal of Biological Chemistry. 277 (24): 21624–9. doi:10.1074/jbc.M202942200. PMID 11948193.
  6. Vincent HA, Deutscher MP (October 2006). "Substrate recognition and catalysis by the exoribonuclease RNase R". The Journal of Biological Chemistry. 281 (40): 29769–75. doi:10.1074/jbc.M606744200. PMID 16893880.


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