RNase R

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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[edit]

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[edit]

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[edit]

  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 3949413Freely accessible. PMID 24653719. 
  3. ^ a b c 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. ^ a b 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 4100097Freely accessible. 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.