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Exonuclease
- 1. EXONUCLEASE Presented by, Amarthya Siddhartha ShryliK S VIIth Sem Molecular Biology Yuvaraja’s College (Autonomous), Mysuru
- 2. Contents • Introduction • TheDNA Exonuclease • Exonuclease of E. coli • Significance to polymerase • Exonuclease of Human • Deficiencies related to exonuclease • Conclusion • References
- 3. Introduction Enzymes as toolsin Genetic Engineering. a) Nucleases: DNases, RNases, exonucleases, endonucleases, restriction endonucleases, isoschizomers. b) DNA polymerase, klenow fragment, reversetransriptase, ligases, S1 nuclease. c) DNA modifying enzymes: polynucleotide kinase, terminal transferase, phosphorylase & phosphatase.Glycosylases,ribonuclease inhibitors, topoisomerases. What is Genetic Engineering?
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- 5. DNA-degrading enzymes Enzymes thatdigest DNA can be divided into the endonucleases and exonucleases. Endonucleases can degrade DNA from the sugar– phosphate backbone to yield nicks in double-stranded DNA. In principle, this can be general or sequence specific (for example, restriction endonucleases). Moreover, some endonucleases are specific for cutting single-stranded DNA. Exonucleases, on the other hand, can degrade DNA from its end — either from the 3′ terminus (3′–5′ direction) or from the 5′ terminus (5′– 3′ direction). The power of the 3′–5′ proofreading exonucleases lies in their capacity to remove the sugar–phosphate backbone from the 3′ end when the bases are not properly paired according to the Watson–Crick base-pair rules (A–T and G–C), when bases are damaged, when they are missing, or even, in some situations, when nucleotides are correctly base-paired.
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- 10. Deficiencies related toExonuclease 3
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- 12. References • Lehman IR,Nussbaum AL (August 1964). "The deoxyribonucleases of Escherichia Coli. V. on the specificity of exonuclease I (Phosphodiesterase)". J. Biol. Chem. 239 (8): 2628–36 • Paul D. Boyer (1952). The Enzymes (1st ed.). Academic Press. p. 211. • Rogers SG, Weiss B (1980). "Exonuclease III of Escherichia coli K-12, an AP endonuclease". Meth. Enzymol. Methods in Enzymology. • West S, Gromak N, Proudfoot NJ (November 2004). "Human 5' → 3' exonuclease Xrn2 promotes transcription termination at co- transcriptional cleavage sites". Nature. 432 • Igor V. Shevelev and Ulrich Hübscher THE 3′–5′ EXONUCLEASES Nature Publishing Group VOLUME 3 MAY 2002
Editor's Notes
- #4 Explain what genetic engineering is with and each enzymes with one sentence for each.
- #5 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 (Xrn1), which is a dependent decapping protein; 3′ to 5′ exonuclease, an independent protein; and poly(A)-specific 3′ to 5′ exonuclease.[1][2] 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. And explain the structure from the figure legend.
- #6 Explain the slide as it is
- #7 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.[4] 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. [5] 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 (later found to be called endonuclease II).[6] 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 than exonuclease I.[7] Exonuclease V is a 3' to 5' hydrolyzing enzyme that catalyzes linear double-stranded DNA and single-stranded DNA, which requires Ca2+.[8] 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. Explain in relation to the table
- #8 Explain the figure from the legend.
- #9 RNA polymerase 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.[3] 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. If needed add a couple of lines from the paper.
- #10 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) Xrn1 continues to further breakdown the product until it is completely degraded.[9] This allows the nucleotides to be recycled. Xrn1 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. Explain the table, say the name it’s yeast homologous, mention the polarity of EXO 1 since it’s different and their functions.
- #11 Explain the table in sentences. For more details refer the paper.
- #12 At least eight human autonomous 3′–5′ exonucleases — TREX1, TREX2, p53, MRE11, RAD1, RAD9, APE1 and VDJP — have been identified in the past five years. However, three of them (TREX2, RAD1 and RAD9) have been characterized only as recombinant proteins, and our knowledge of their biochemical properties, post-translational modifications, interaction with other proteins and physiological function is still limited. On the other hand, many of these enzymes have been shown to have an important function in accurate DNA replication, effective DNA repair and DNA recombination. Mutations in the genes that encode these 3′–5′ exonucleases lead to dramatic consequences in vivo — strong mutator phenotypes, cancer susceptibility and even inviability. A particular 3′–5′ exonuclease might, therefore, have more than one function in the cell, and a particular DNA metabolic event might require more than one 3′–5′ exonuclease activity. A similar redundancy of function has previously been proposed for DNA polymerases36. The role of autonomous 3′–5′ exonucleases in maintaining genomic stability in mammalian cells is particularly relevant with respect to the development of anticancer and antiviral therapies. Overexpression of a 3′–5′ exonuclease in human cells might also be connected to increased longevity owing to stabilization of the mutation rates in a cell. We will probably soon learn more about how these exonucleases act in DNA replication, DNA repair, DNA recombination, checkpoint control, V(D)J recombination and, perhaps, even sister chromatid cohesion. The surprising finding that, under certain circumstances (such as post-translational modifications and/or association with other factors), well known proteins will adopt 3′–5′ exonuclease activities might continue. After all, the many insults that DNA faces in every cell each day imply an enormous redundancy under both normal conditions and even more so in situations of genotoxic stress.
- #13 Add references from Wikipedia references and this paper. Change figure and table numbers.