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.{{cite journal | vauthors = Cheng ZF, Deutscher MP | title = An important role for RNase R in mRNA decay | journal = Molecular Cell | volume = 17 | issue = 2 | pages = 313–8 | date = January 2005 | pmid = 15664199 | doi = 10.1016/j.molcel.2004.11.048 | doi-access = free }}{{cite journal | vauthors = Venkataraman K, Guja KE, Garcia-Diaz M, Karzai AW | title = Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue | journal = Frontiers in Microbiology | volume = 5 | pages = 93 | date = 2014 | pmid = 24653719 | pmc = 3949413 | doi = 10.3389/fmicb.2014.00093 | doi-access = free }} 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.{{cite journal | vauthors = Domingues S, Moreira RN, Andrade JM, Dos Santos RF, Bárria C, Viegas SC, Arraiano CM | title = The role of RNase R in trans-translation and ribosomal quality control | journal = Biochimie | volume = 114 | pages = 113–8 | date = July 2015 | pmid = 25542646 | doi = 10.1016/j.biochi.2014.12.012 }}
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.
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.
RNA digestion
RNase R has two cold shock domains, an RNase catalytic domain, an S1 domain and a basic domain.{{cite journal | vauthors = Suzuki H, Tsukahara T | title = A view of pre-mRNA splicing from RNase R resistant RNAs | journal = International Journal of Molecular Sciences | volume = 15 | issue = 6 | pages = 9331–42 | date = May 2014 | pmid = 24865493 | pmc = 4100097 | doi = 10.3390/ijms15069331 | doi-access = free }}
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.{{cite journal | vauthors = Cheng ZF, Deutscher MP | title = Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II | journal = The Journal of Biological Chemistry | volume = 277 | issue = 24 | pages = 21624–9 | date = June 2002 | pmid = 11948193 | doi = 10.1074/jbc.M202942200 | doi-access = free }} Besides the substrate RNAs that construct double-stranded RNA with 3' overhangs shorter than seven nucleotides, RNase R can degrade all linear RNAs.{{cite journal | vauthors = Vincent HA, Deutscher MP | title = Substrate recognition and catalysis by the exoribonuclease RNase R | journal = The Journal of Biological Chemistry | volume = 281 | issue = 40 | pages = 29769–75 | date = October 2006 | pmid = 16893880 | doi = 10.1074/jbc.M606744200 | doi-access = free }} 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.