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Ribonuclease
 
 
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Ribonuclease (commonly abbreviated RNase) is a type of nuclease
Nuclease

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older papers may use terms such as "polynucleotidase" or "nucleodepolymerase"....
 that catalyzes
Catalysis

Catalysis is the process in which the reaction rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst....
 the degradation of RNA
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
 into smaller components. Ribonucleases can be divided into endoribonuclease
Endoribonuclease

A Endoribonuclease is a ribonuclease endonuclease. Example includes both single proteins like RNase III, RNase A, RNase T1 and RNase H but also, complexes of proteins like RNase P and the RNA-induced silencing complex....
s and exoribonuclease
Exoribonuclease

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

organisms studied contain many RNases of many different classes, showing that RNA degradation is a very ancient and important process.






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Encyclopedia


Ribonuclease (commonly abbreviated RNase) is a type of nuclease
Nuclease

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older papers may use terms such as "polynucleotidase" or "nucleodepolymerase"....
 that catalyzes
Catalysis

Catalysis is the process in which the reaction rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst....
 the degradation of RNA
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
 into smaller components. Ribonucleases can be divided into endoribonuclease
Endoribonuclease

A Endoribonuclease is a ribonuclease endonuclease. Example includes both single proteins like RNase III, RNase A, RNase T1 and RNase H but also, complexes of proteins like RNase P and the RNA-induced silencing complex....
s and exoribonuclease
Exoribonuclease

An exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or 3' end of the RNA molecule....
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 many different classes, showing that RNA degradation is a very ancient and important process. As well as cleaning 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 a 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. It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping
5' cap

The 5' cap is a specially altered nucleotide on the 5' end of precursor messenger RNA and some other primary RNA transcripts as found in eukaryotes and, as a special exception, caliciviruses such as norovirus....
, 3' end polyadenylation
Polyadenylation

Polyadenylation is the addition of a poly tail, a stretch of RNA where all the nucleobase are adenines, onto an RNA molecule. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA for translation ....
, and folding within an RNA protein complex (ribonucleoprotein
Ribonucleoprotein

Ribonucleoprotein is a nucleoprotein that contains RNA, i.e. it is an association that combines ribonucleic acid and protein together. A few examples are known like the ribosome, the enzyme telomerase and small nuclear RNPs which are implicated in pre-mRNA splicing and are among the main components of the nucleolus....
 particle or RNP).

Another mechanism of protection is ribonuclease inhibitor
Ribonuclease inhibitor

Ribonuclease inhibitor is a large , acidic , leucine-rich repeat protein that forms extremely tight complexes with certain ribonucleases. It is a major cellular protein, comprising ~0.1% of all cellular protein by weight, and appears to play an important role in regulating the lifetime of RNA....
 (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
Protein-protein interaction

Protein-protein interactions involve the association of protein molecules. These associations are studied from the perspective of biochemistry, signal transduction and graph theory....
; the dissociation constant
Dissociation constant

In chemistry and biochemistry, a dissociation constant is a specific type of equilibrium constant that measures the propensity of a larger object to separate reversibly into smaller components, as...
 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
Restriction enzyme

A restriction enzyme is an enzyme that cuts double-stranded or single stranded DNA at specific recognition nucleotide sequences known as restriction sites....
s, which cleave highly specific sequences of double-stranded DNA
DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetics instructions used in the development and functioning of all known living organisms and some viruses....
, a variety of endoribonuclease
Endoribonuclease

A Endoribonuclease is a ribonuclease endonuclease. Example includes both single proteins like RNase III, RNase A, RNase T1 and RNase H but also, complexes of proteins like RNase P and the RNA-induced silencing complex....
s 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

Angiogenesis is a physiological process involving the growth of new blood vessels from pre-existing vessels. Though there has been some debate over this, vasculogenesis is the term used for spontaneous blood-vessel formation, and Intussusception is the term for new blood vessel formation by splitting off existing ones....
 and self-incompatibility in flowering plant
Flowering plant

The flowering plants or angiosperms are the most widespread group of Embryophytes. The flowering plants and the gymnosperms are the only extant groups of Spermatophyte....
s (angiosperms). Also, RNases in prokaryotic toxin-antitoxin systems are proposed to function as plasmid
Plasmid

File:plasmid .svgA plasmid is an extra-chromosomal DNA molecule separate from the chromosome which is capable of replicating independently of the chromosomal DNA....
 stability loci, and as stress-response elements when present on the chromosome.

Classification


Major types of endoribonucleases

Rnase A
RNase A
Ribonuclease A

Ribonuclease A is an endonuclease that cleaves single-stranded RNA. Bovine pancreatic RNase A is one of the classic model systems of protein science....
 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
Denaturation (biochemistry)

Denaturation is a process in which proteins or nucleic acids lose their structure by application of some external stress or compound for example, treatment of proteins with strong acids or bases, high concentrations of inorganic salts, organic compound solvents , or heat....
. It is sequence specific for single-stranded RNAs. It cleaves 3'end of unpaired C and U residues, leaving a 3'-phosphorylated product, via a 2',3'-cyclic monophosphate.


RNase H
RNase H

The enzyme RNase H is a ribonuclease that cleaves the 3'-O-P-bond of RNA in a DNA/RNA duplex to produce 3'-hydroxyl and 5'-phosphate terminated products....
 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
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     3.1.??: RNase I cleaves 3'-end of ssRNA at all dinucleotide bonds leaving a 5' hydroxyl, and 3' phosphate, via a 2',3'-cyclic monophosphate intermediate.


RNase III
RNase III

RNase III enzymes specifically bind to and cleave double-stranded RNA . There are three subdivisions, known as Class 1, 2, and 3.* Class 1 RNases III are largely found in bacteria, bacteriophage, and some fungi....
 is a type of ribonuclease that cleaves rRNA (16s rRNA and 23s rRNA) from transcribed polycistronic RNA operon in prokaryotes. It also digests double strands RNA (dsRNS)-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
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     3.1.??: RNase L
    RNAse L

    RNase L is an interferon-induced ribonuclease which, upon activation, destroys all RNA within the cell ....
     is an interferon-induced nuclease which, upon activation, destroys all RNA within the cell


RNase P
RNase P

Ribonuclease P is a type of Ribonuclease which cleaves RNA. RNase P is unique from other Ribonuclease in that it is a ribozyme ? a RNA that acts as a catalyst in the same way that a protein based enzyme would....
 is a type of ribonuclease that is unique in that it is a ribozyme
Ribozyme

A ribozyme is an RNA molecule that catalyzes a chemical reaction. Many natural ribozymes catalyze either the hydrolysis of one of their own phosphodiester bonds, or the hydrolysis of bonds in other RNAs, but they have also been found to catalyze the aminotransferase activity of the ribosome....
 – a ribonucleic acid
RNA

Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
 that acts as a catalyst in the same way as an enzyme
Enzyme

Enzymes are biomolecules that catalysis chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called Substrate , and the enzyme converts them into different molecules, the products....
. Its function is to cleave off an extra, or precursor, sequence on tRNA molecules. RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome
Ribosome

Ribosomes are complexes of RNA and protein that are found in all cell s. Ribosomes from bacteria, archaea and eukaryotes, the three domains of life on Earth, have significantly different structure and RNA....
). A form of RNase P that is a protein
Protein

Proteins are organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid Residue ....
 and does not contain RNA has recently been discovered.


  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     3.1.??: RNase PhyM
    RNase PhyM

    RNase PhyM is a type of endoribonuclease which is sequence specific for single stranded RNAs. It cleaves 3'-end of unpaired A and U residues....
     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 V1 is non-sequence specific for double-stranded RNAs. It cleaves base-paired nucleotide residues.


RNase V


Major types of exoribonucleases

  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     : Polynucleotide Phosphorylase (PNPase) functions as an exonuclease
    Exonuclease

    Exonucleases are enzymes that cleave nucleotides one at a time from an end of a polynucleotide chain. These enzymes hydrolyze phosphodiester bonds from either the 3' or 5' terminus of a polynucleotide molecule....
     as well as a nucleotidyltransferase
    Nucleotidyltransferase

    Nucleotidyltransferases are phosphotransferase enzymes which act upon components of nucleotides.They are classified under EC number 2.7.7....
    .


  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     : RNase PH
    RNase PH

    RNase PH is an 3'-5' exoribonuclease and nucleotidyltransferase, present in archaea and bacteria, that is involved in tRNA processing. Contrary to hydrolytic enzymes, it is a phosphorolytic enzyme, meaning that it uses inorganic phosphate as a cofactor to cleave nucleotide-nucleotide bonds, releasing diphosphate nucleotides....
     functions as an exonuclease
    Exonuclease

    Exonucleases are enzymes that cleave nucleotides one at a time from an end of a polynucleotide chain. These enzymes hydrolyze phosphodiester bonds from either the 3' or 5' terminus of a polynucleotide molecule....
     as well as a nucleotidyltransferase
    Nucleotidyltransferase

    Nucleotidyltransferases are phosphotransferase enzymes which act upon components of nucleotides.They are classified under EC number 2.7.7....
    .


  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     3.1.??: RNase II is responsible for the processive 3'-to-5' degradation of single-stranded RNA
    RNA

    Ribonucleic acid is a type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate....
    .


  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     3.1.??: RNase R
    RNase R

    RNase R is an 3'-5' exoribonuclease closely related to RNase II, which has been shown to be involved in mRNA degradation in bacteria. RNase R has homologues in many other organisms....
     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 number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     : RNase D
    RNase D

    RNase D is one of the seven exoribonucleases identified in E. coli. It is an 3'-5' exoribonuclease and which has been shown to be involved in the 3' processing of various stable RNA molecules....
     is involved in the 3'-to-5' processing of pre-tRNA
    Transfer RNA

    Transfer RNA is a small RNA that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation ....
    s.


  • EC number
    EC number

    The Enzyme Commission number is a numbering scheme scheme for enzymes, based on the chemical reactions they catalysis.As a system of enzyme nomenclature, every EC number is associated with a recommended name for the respective enzyme....
     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.


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