Exonuclease
Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end 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 of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5′ to 3′ exonuclease (Xrn1), which is a dependent decapping protein; 3′ to 5′ exonuclease, an independent protein; and poly-specific 3′ to 5′ exonuclease.
In both archaea 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.
Significance to polymerase
RNA polymerase II is known to be in effect during transcriptional termination; it works with a 5' exonuclease 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 3' to 5' and 5' to 3' exonuclease activity, which is used in editing and proofreading DNA for errors. The 3' to 5' can only remove one mononucleotide at a time, and the 5' to 3' activity can remove mononucleotides or up to 10 nucleotides at a time.
''E. coli'' types
In 1971, Lehman IR discovered exonuclease I in E. coli. Since that time, there have been numerous discoveries including: exonuclease, II, III, 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:
- 3' to 5' exodeoxyribonuclease activity, which is specific for double-stranded DNA
- RNase activity
- 3' phosphatase activity
- AP endonuclease activity.
Exonuclease V is a 3' to 5' hydrolyzing enzyme that catalyzes linear double-stranded DNA and single-stranded DNA, which requires Ca2+. This enzyme is extremely important in the process of homologous recombination.
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.
dnaQ
In Escherichia coli the dnaQ gene encodes the ε subunit of DNA polymerase III. The ε subunit is one of three core proteins of the DNA polymerase complex. It acts as a 3'→5' DNA directed proofreading exonuclease that removes incorrectly incorporated bases during replication. Similarly, in Salmonella typhimurium bacteria, the 3' to 5' editing function employed during DNA replication is also encoded by a gene, dnaQ, which specifies a 3' to 5' exonuclease subunit, one of the three separately encoded core proteins of the DNA polymerase III holoenzyme.In contrast to E. coli and S. typhimurium, where the polymerase and editing functions are encoded by separate genes, in the bacterial species Buchnera aphidicola the DNA polymerase encoded by the DNA III gene contains both DNA polymerase and 3' to 5' exonuclease domains. An evolutionary divergence, appears to have been associated with the separation of the DNA polymerase gene function from the 3' to 5' exonuclease editing gene function in the lineage that led to E. coli and S. typhimurium.