Ribonuclease (commonly abbreviated RNase) is a type of

nuclease In biochemistry, a nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds that link nucleotides together to form nucleic acids. Nucleases variously affect single and ...

that catalyzes the degradation of

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

into smaller components. Ribonucleases can be divided into endoribonucleases and

exoribonuclease An exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or the 3' end of the RNA molecule. Enzymes that remove nucleotides from the 5' end are called ''5'-3 ...

s, and comprise several sub-classes within the EC 2.7 (for the phosphorolytic enzymes) and 3.1 (for the hydrolytic enzymes) classes of enzymes.

Function

All organisms studied contain many RNases of two different classes, showing that RNA degradation is a very ancient and important process. As well as clearing of cellular RNA that is no longer required, RNases play key roles in the maturation of all RNA molecules, both messenger RNAs that carry genetic material for making proteins and non-coding RNAs that function in varied cellular processes. In addition, active RNA degradation systems are the first defense against RNA viruses and provide the underlying machinery for more advanced cellular immune strategies such as RNAi. 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 including 5' end capping, 3' end

polyadenylation Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In euka ...

, formation of an RNA·RNA duplex, and folding within an RNA protein complex (

ribonucleoprotein Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins. Structures Nucleoproteins tend to be positively charged, facilitating inter ...

particle or RNP). Another mechanism of protection is ribonuclease inhibitor (RI), which comprises a relatively large fraction of cellular protein (~0.1%) in some cell types, and which binds to certain ribonucleases with the highest affinity of any protein-protein interaction; the

dissociation constant In chemistry, biochemistry, and pharmacology, a dissociation constant (''K''D) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex ...

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. Similar to

restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

s, which cleave highly specific sequences of double-stranded

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

, a variety of endoribonucleases that recognize and cleave specific sequences of single-stranded RNA have been recently classified. RNases play a critical role in many biological processes, including

angiogenesis Angiogenesis is the physiological process through which new blood vessels form from pre-existing vessels, formed in the earlier stage of vasculogenesis. Angiogenesis continues the growth of the vasculature mainly by processes of sprouting and ...

and self-incompatibility in

flowering plant Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (). The term angiosperm is derived from the Ancient Greek, Greek words (; 'container, vessel') and (; 'seed'), meaning that the seeds are enclosed with ...

s (angiosperms). Many stress-response toxins of prokaryotic

toxin-antitoxin system A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed ...

s have been shown to have RNase activity and homology.

Classification

Major types of endoribonucleases

* : RNase A is an RNase that is commonly used in research. RNase A (''e.g.'', bovine pancreatic ribonuclease A: ) 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 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. It does not require any cofactors for its activity. * : 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. * : 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 * : RNase P is a type of ribonuclease that is unique in that it is a

ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to Catalysis, catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozy ...

– a

ribonucleic acid Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins ( messenger RNA). RNA and deoxyr ...

that acts as a catalyst in the same way as an

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

. One of its functions is to cleave off a leader sequence from the 5' end of one stranded pre-

tRNA Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...

. RNase P is one of two known multiple turnover ribozymes in nature (the other being the

ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...

). 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 a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

and does not contain RNA has recently been discovered. * EC number 3.1.??: RNase PhyM is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A and U residues. * : RNase T1 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired G residues. * : RNase T2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of all 4 residues, but preferentially 3'-end of As. * : RNase U2 is sequence specific for single-stranded RNAs. It cleaves 3'-end of unpaired A residues. * : RNase V is specific for polyadenine and polyuridine RNA. * : 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. * : 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.

Major types of exoribonucleases

* EC number : Polynucleotide Phosphorylase (PNPase) functions as an

exonuclease Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is th ...

as well as a nucleotidyltransferase. * EC number : RNase PH functions as an

as well as a nucleotidyltransferase. * 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 : 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. * : Oligoribonuclease degrades short oligonucleotides to mononucleotides. * : Exoribonuclease I degrades single-stranded RNA from 5'-to-3', exists only in eukaryotes. * : Exoribonuclease II is a close homolog of Exoribonuclease I.

RNase specificity

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, recently

CRISPR CRISPR (; acronym of clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic CRISPR is d ...

/Cas system natively recognizing and cutting DNA was engineered to cleave ssRNA in a sequence-specific manner.

RNase contamination during RNA extraction

The extraction 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 neutralizing DNases. 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. For example, RNase 7, a member of the RNase A superfamily, is secreted by human skin and serves as a potent antipathogen defence. 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.

References

Ahmed TAE, Udenigwe CC, Gomaa A. Editorial: Biotechnology and Bioengineering Applications for Egg-Derived Biomaterials. Front Bioeng Biotechnol. 2021 Sep 20;9:756058

Sources

* D'Alessio G and Riordan JF, eds. (1997) ''Ribonucleases: Structures and Functions'', Academic Press. * Gerdes K, Christensen SK and Lobner-Olesen A (2005). "Prokaryotic toxin-antitoxin stress response loci". ''Nat. Rev. Microbiol.'' (3) 371–382.

External links

IUBMB Enzyme Database for EC 3.1

Integrated Enzyme Database for EC 3.1
{{Portal bar, Biology, border=no EC 3.1 EC 3.1.26 EC 3.1.27