Ribonuclease

Ribonuclease, abbreviated commonly as RNase, is a nuclease that catalyzes the hydrolysis of RNA into smaller components. They can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.

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Function

RNases are extremely common, resulting in very short lifespans for any RNA that is not in a protected environment. One mechanism of protection is ribonuclease inhibitor (RI), which comprises a relatively large fraction of cellular protein (~0.1%) and which binds to certain ribonucleases with the highest affinity of any protein-protein interaction; the dissociation constant for the RI-RNase A complex is ~20 fM under physiological conditions. RI is used in most laboratories that study RNA to protect their samples against degradation from environmental RNases.

Perhaps surprisingly, RNases tend to be insensitive to the cleaved sequence. There appear to be no RNase analogs of the restriction enzymes, which cleave highly specific sequences of double-stranded DNA. This deficit may be overcome using RNase H and single-stranded DNA complementary to the desired cleavage sequence.

RNases play a critical role in many biological processes, including angiogenesis and self-incompatibility in flowering plants (angiosperms).

Classification

Major types of endoribonucleases

• EC 3.1.27.5: RNase A is an RNase that is commonly used in research. RNase A (e.g., bovine pancreatic ribonuclease A: PDB 2AAS) is one of the hardiest enzymes in common laboratory usage; one method of isolating it is to boil a crude cellular extract until all enzymes other than RNase A are denatured. It is sequence specific for single stranded RNAs. It cleaves 3'end of unpaired C and U residues, leaving a 3'-phosphorylated product.

• EC 3.1.26.4: RNase H is a ribonuclease that cleaves the RNA in a DNA/RNA duplex to produce ssDNA. RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism, aided by an enzyme-bound divalent metal ion. RNase H leaves a 5'-phosphorylated product.

• EC number 3.1.??: RNase I cleaves 3'-end of ssRNA at all dinucleotide bonds leaving a 5´ hydroxyl, 2',3'-cyclic monophosphate.

• EC 3.1.26.3: RNase III is a type of ribonuclease that cleaves rRNA (16s rRNA and 23s rRNA) from transcribed polycistronic RNA operon in prokaryotes.

• EC number 3.1.??: RNase L is an interferon-induced nuclease which, upon activation, destroys all RNA within the cell

• EC 3.1.26.5: RNase P is a type of ribonuclease and is currently under heavy research. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Further RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome).

• EC number 3.1.??: RNase PhyM is sequence specific for single stranded RNAs. It cleaves 3'-end of unpaired A and U residues.

• EC 3.1.27.3: RNase T1 is sequence specific for single stranded RNAs. It cleaves 3'-end of unpaired G residues.

• EC 3.1.27.1: RNase T2 is sequence specific for single stranded RNAs. It cleaves 3'-end of all 4 residues, but preferentially 3'-end of As.

• EC 3.1.27.4: RNase U2 is sequence specific for single stranded RNAs. It cleaves 3'-end of unpaired A residues.

• EC 3.1.27.8: RNase V1 is non-sequence specific for double stranded RNAs. It cleaves base-paired nucleotide residues.

• EC 3.1.27.8: RNase V

Major types of exoribonucleases

• EC number EC 2.7.7.8: Polynucleotide Phosphorylase (PNPase) functions both as an exonuclease as well as a nucleotidyltransferase.

• EC number EC 2.7.7.56: RNase PH functions both as an exonuclease as well as a nucleotidyltransferase.

• EC number 3.1.??: RNase II is responsible for the processive 3'-to-5' degradation of single-stranded RNA.

• EC number 3.1.??: RNase R is a close homolog of RNase II, but it can, unlike RNase II, degrade RNA with secondary structures without help of accessory factors.

• EC number EC 3.1.13.5: RNase D is involved in the 3'-to-5' processing of pre-tRNAs.

• EC number 3.1.??: RNase T is the major contributor for the 3'-to-5' maturation of many stable RNAs.

• EC 3.1.13.3: Oligoribonuclease degrades short oligonucleotides to mononucleotides.

• EC 3.1.11.1: Exoribonuclease I degrades single-stranded RNA from 5'-to-3', exists only in eukaryotes.

• EC 3.1.13.1: Exoribonuclease II is a close homolog of Exoribonuclease I.

• Integrated Enzyme Database for EC 3.1

References

• D'Alessio G and Riordan JF, eds. (1997) Ribonucleases: Structures and Functions, Academic Press.