Ribonuclease (commonly abbreviatedRNase) is a type ofnuclease thatcatalyzes the degradation ofRNA into smaller components. Ribonucleases can be divided intoendoribonucleases andexoribonucleases, and comprise several sub-classes within theEC 2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.
Ribonucleases are found in all domains of life as well as in viruses. While some families of RNases, such as EndoU-like RNases, are ubiquitous, others, such asRNase A, are only found in a subset of vertebrates.[2] RNases play a role in a multitude of processes including antiviral defense, mRNA regulation, RNA maturation ofcoding andnoncoding RNA,RNA interference andreplication inretroviruses.[3]
Some cells also secrete copious quantities of non-specific RNases such as A and T1. RNases are, therefore, extremely common, resulting in very short lifespans for any RNA that is not in a protected environment. All intracellular RNAs are protected from RNase activity by a number of strategies including5' end capping, 3' endpolyadenylation, formation of an RNA·RNA duplex, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).[citation needed]
Another mechanism of protection isribonuclease inhibitor (RI), which binds to certain ribonucleases with the highest affinity of anyprotein-protein interaction; thedissociation constant for the RI-RNase A complex is between 10-14 and 10-16 M under physiological conditions.[4] Recombinant RNase inhibitors (RRIs), which are in-vitro synthesized RI, are used in most laboratories that study RNA to protect their samples against degradation from environmental RNases.[5]
Similar torestriction enzymes, which cleave highly specific sequences of double-strandedDNA, a variety ofendoribonucleases that recognize and cleave specific sequences of single-stranded RNA have been recently classified.[6]
EC4.6.1.18: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 aredenatured. It is specific for single-stranded RNAs. It cleaves the 3'-end of unpaired C and U residues, ultimately forming a 3'-phosphorylated product via a 2',3'-cyclic monophosphate intermediate.[10][11] It does not require any cofactors for its activity.[12]
EC3.1.26.4: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.[13]
EC3.1.26.3:RNase III is a type of ribonuclease that cleaves rRNA (16s rRNA and 23s rRNA) from transcribed polycistronic RNA operon in prokaryotes. It also digests double-stranded RNA (dsRNA)-Dicer family of RNAse, cutting pre-miRNA (60–70bp long) at a specific site and transforming it in miRNA (22–30bp), that is actively involved in the regulation of transcription and mRNA life-time.
EC number 3.1.26.-??:RNase L is an interferon-induced nuclease that, upon activation, destroys all RNA within the cell
EC3.1.26.5:RNase P is a type of ribonuclease that is unique in that it is aribozyme – aribonucleic acid that acts as a catalyst in the same way as anenzyme. One of its functions is to cleave off a leader sequence from the 5' end of one stranded pre-tRNA. RNase P is one of two known multiple turnover ribozymes in nature (the other being theribosome). In bacteria RNase P is also responsible for the catalytic activity of holoenzymes, which consist of an apoenzyme that forms an active enzyme system by combination with a coenzyme and determines the specificity of this system for a substrate. A form of RNase P that is aprotein and does not contain RNA has recently been discovered.[14]
EC number 3.1.??:RNase PhyM is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A and U residues.
EC4.6.1.24:RNase T1 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired G residues.
EC4.6.1.19:RNase T2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of all 4 residues, but preferentially 3'-end of As.
EC4.6.1.20:RNase U2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A residues.
EC3.1.26.12:RNase E is a ribonuclease of plant origin, which modulates SOS responses in bacteria, for a response to the stress of DNA damage by activation of the SOS mechanism by the RecA/LexA dependent signal transduction pathway that transcriptionally depresses a multiplicity of genes leading to transit arrest of cell division as well as initiation of DNA repair.[15]
EC3.1.26.-:RNase G It is involved in processing the 16'-end of the 5s rRNA. It is related to chromosome separation and cell division. It is considered one of the components of cytoplasmic axial filament bundles. It is also thought that it can regulate the formation of this structure.[16]
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.
The active site looks like a rift valley where all the active site residues create the wall and bottom of the valley. The rift is very thin and the small substrate fits perfectly in the middle of the active site, which allows for perfect interaction with the residues. It actually has a little curvature to the site which the substrate also has. Although usually most exo- and endoribonucleases are not sequence specific, recentlyCRISPR/Cas system natively recognizing and cutting DNA was engineered to cleave ssRNA in a sequence-specific manner.[17]
Theextraction of RNA in molecular biology experiments is greatly complicated by the presence of ubiquitous and hardy ribonucleases that degrade RNA samples. Certain RNases can be extremely hardy and inactivating them is difficult compared to neutralizingDNases. In addition to the cellular RNases that are released, there are several RNases that are present in the environment. RNases have evolved to have many extracellular functions in various organisms.[18][19][20] For example, RNase 7, a member of theRNase A superfamily, is secreted by human skin and serves as a potent antipathogen defence.[21][22] In these secreted RNases, the enzymatic RNase activity may not even be necessary for its new,exapted function. For example, immune RNases act by destabilizing the cell membranes of bacteria.[23][24]
^Noguchi S (July 2010). "Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate".Acta Crystallographica D.66 (Pt 7):843–9.doi:10.1107/S0907444910019621.PMID20606265.
^Shamsher S. Kanwar*, Puranjan Mishra, Khem Raj Meena, Shruti Gupta and Rakesh Kumar, Ribonucleases and their Applications, 2016, Journal of Advanced Biotechnology and Bioengineering
^Wachi M, Umitsuki G, Shimizu M, Takada A, Nagai K. Escherichia coli cafA gene encodes a novel RNase, designated as RNase G, involved in processing of the 5' end of 16S rRNA. Biochem Biophys Res Commun. 1999;259(2):483‐488. doi:10.1006/bbrc.1999.0806
