Exonuclease
Encyclopedia
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 the endonuclease
, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5’ to 3’ exonuclease, which is a dependent decapping protein, 3’ to 5’ exonuclease, an independent protein, and poly(A)-specific 3’ to 5’ exonuclease.
In both archaebacteria and eukaryotes, one of the main routes of RNA degradation is performed by the multi-protein exosome
complex, which consists largely of 3' to 5' exoribonucleases.
II is known to be in effect during transcriptional termination; it works with a 5’ exonuclease (human gene Xrn2) to degrade the newly formed transcript downstream, leaving the polyadenylation site and simultaneously shooting the polymerase. This process involves the exonuclease's catching up to the pol II and terminating the transcription.
Pol I then synthesizes DNA nucleotides in place of the RNA primer it had just removed. DNA polymerase I also has 5' to 3' exonuclease activity, which is used in editing and proofreading DNA for errors.
, IV, V
, VI, VII
, and VIII. Each type of exonuclease has a specific type of function or requirement.
Exonuclease I breaks apart single-stranded DNA in a 3'=>5' direction, releasing deoxyribonucleoside 5'-monophosphates one after another. It does not cleave DNA strands without terminal 3'-OH groups because they are blocked by phosphoryl or acetyl groups.
Exonuclease II is associated with DNA polymerase I, which contains a 5' exonuclease that clips off the RNA primer contained immediately upstream from the site of DNA synthesis in a 5' → 3' manner.
Exonuclease III
has four catalytic activities:
Exonuclease IV adds a water molecule, so it can break the bond of an oligonucleotide to nucleoside 5’ monophosphate. This exonuclease requires Mg 2+ in order to function and works at higher temperatures then exonuclease I.
Exonuclease V is a 3’ to 5’ hydrolyzing enzyme that catalyzes linear double-stranded DNA and single-stranded DNA, which requires Ca2+.
Exonuclease VIII is 5’ to 3’ dimeric protein that does not require ATP or any gaps or nicks in the strand, but requires a free 5’ OH group to carry out its function.
that is found to be associated with mRNA metabolism, transcription initiation, and mRNA degradation. CCR4 has been found to contain RNA
and single-stranded DNA
3’to 5’ exonuclease activities. Another component associated with the CCR4 complex is CAF1 protein, which has been found to contain 3’to 5’ or 5’ to 3’ exonuclease domains in Mus musculus and Caenorhabditis elegans
. This protein has not been found in yeast, which suggests that it is likely to have an abnormal exonuclease domain like the one seen in a metazoan. Yeast contains Rat1 and Xrn1 exonuclease. The Rat1 works just like the human type (Xrn2) and Xrn1 function in the cytoplasm is in the 5’ to 3’ direction to degrade RNAs (pre-5.8s and 25s rRNAs) in the absence of Rat1.
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs. Its close relative is the endonuclease
Endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain. Typically, a restriction site will be a palindromic sequence four to six nucleotides long. Most...
, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5’ to 3’ exonuclease, which is a dependent decapping protein, 3’ to 5’ exonuclease, an independent protein, and poly(A)-specific 3’ to 5’ exonuclease.
In both archaebacteria and eukaryotes, one of the main routes of RNA degradation is performed by the multi-protein exosome
Exosome
Exosome can refer to:* Exosome complex - a macromolecular complex involved in RNA degradation* Exosome - a vesicle secreted by mammalian cells...
complex, which consists largely of 3' to 5' exoribonucleases.
Significance to polymerase
RNA polymerasePolymerase
A polymerase is an enzyme whose central function is associated with polymers of nucleic acids such as RNA and DNA.The primary function of a polymerase is the polymerization of new DNA or RNA against an existing DNA or RNA template in the processes of replication and transcription...
II is known to be in effect during transcriptional termination; it works with a 5’ exonuclease (human gene Xrn2) to degrade the newly formed transcript downstream, leaving the polyadenylation site and simultaneously shooting the polymerase. This process involves the exonuclease's catching up to the pol II and terminating the transcription.
Pol I then synthesizes DNA nucleotides in place of the RNA primer it had just removed. DNA polymerase I also has 5' to 3' exonuclease activity, which is used in editing and proofreading DNA for errors.
E. coli types
In 1971, Lehman IR discovered exonuclease I in E. coli. Since that time, there have been numerous discoveries including: exonuclease, II, IIIExonuclease III
Exonuclease III is an enzyme that belongs to the exonuclease family. ExoIII catalyzes the stepwise removal of mononucleotides from 3´-hydroxyl termini of duplex DNA...
, IV, V
RecBCD
RecBCD, also known as Exonuclease V, is an enzyme of the E. coli bacterium that initiates recombinational repair from potentially lethal double strand breaks in DNA which may result from ionizing radiation, replication errors, endonucleases, oxidative damage, and a host of other factors...
, VI, VII
Exonuclease VII
In molecular biology, exonuclease VII is a bacterial exonuclease enzyme. It is composed of two nonidentical subunits; one large subunit and 4 small ones. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also...
, and VIII. Each type of exonuclease has a specific type of function or requirement.
Exonuclease I breaks apart single-stranded DNA in a 3'=>5' direction, releasing deoxyribonucleoside 5'-monophosphates one after another. It does not cleave DNA strands without terminal 3'-OH groups because they are blocked by phosphoryl or acetyl groups.
Exonuclease II is associated with DNA polymerase I, which contains a 5' exonuclease that clips off the RNA primer contained immediately upstream from the site of DNA synthesis in a 5' → 3' manner.
Exonuclease III
Exonuclease III
Exonuclease III is an enzyme that belongs to the exonuclease family. ExoIII catalyzes the stepwise removal of mononucleotides from 3´-hydroxyl termini of duplex DNA...
has four catalytic activities:
- 3’ to 5’ exodeoxyribonuclease activity, which is specific for double-stranded DNA
- RNase activity
- 3’ phosphate activity
- AP endonuclease activity (later found to be called endonuclease II).
Exonuclease IV adds a water molecule, so it can break the bond of an oligonucleotide to nucleoside 5’ monophosphate. This exonuclease requires Mg 2+ in order to function and works at higher temperatures then exonuclease I.
Exonuclease V is a 3’ to 5’ hydrolyzing enzyme that catalyzes linear double-stranded DNA and single-stranded DNA, which requires Ca2+.
Exonuclease VIII is 5’ to 3’ dimeric protein that does not require ATP or any gaps or nicks in the strand, but requires a free 5’ OH group to carry out its function.
Discoveries in humans
The 3’ to 5’ human type endonuclease is known to be essential for the proper processing of histone pre-mRNA, in which U7 snRNP directs the single cleavage process. Following the removal of the downstream cleavage product (DCP) 5’ to 3’ exonuclease continues to further breakdown the product until it is completely degraded. This allows the nucleotides to be recycled. 5’ To 3’ exonuclease is linked to a co-transcriptional cleavage (CoTC) activity that acts as a precursor to develop a free 5’ unprotected end, so the exonuclease can remove and degrade the downstream cleavage product (DCP). This initiates transcriptional termination because one does not want DNA or RNA strands building up in their bodies.Discoveries in yeast
CCR4-NOT is a general transcription regulatory complex in yeastYeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
that is found to be associated with mRNA metabolism, transcription initiation, and mRNA degradation. CCR4 has been found to contain RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
and single-stranded DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
3’to 5’ exonuclease activities. Another component associated with the CCR4 complex is CAF1 protein, which has been found to contain 3’to 5’ or 5’ to 3’ exonuclease domains in Mus musculus and Caenorhabditis elegans
Caenorhabditis elegans
Caenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
. This protein has not been found in yeast, which suggests that it is likely to have an abnormal exonuclease domain like the one seen in a metazoan. Yeast contains Rat1 and Xrn1 exonuclease. The Rat1 works just like the human type (Xrn2) and Xrn1 function in the cytoplasm is in the 5’ to 3’ direction to degrade RNAs (pre-5.8s and 25s rRNAs) in the absence of Rat1.