DNA polymerases eukaryotes

Good summary of the properties and roles of the more than one dozen known eukaryotic DNA polymerases. 

Prokaryotic and eukaryotic DNA polymerases elongate a new ChA strand by adding deoxyribonucleotides, one at a time, to the 3-end of the growing chain (see Figure 29.16). The sequence of nucleotides that are added is dictated by the base sequence of fie Figure 29.15 template strand with which the incoming nucleotides are paired. 

At least five classes of eukaryotic DNA polymerases have been identified and categorized on the basis of molecular weight, cellular location, sensitivity to inhibitors, and the templates or substrates on which they act. They are designated by Greek letters rather than Roman numerals (Figure 29.22). 

There are at least five classes of eukaryotic DNA polymerases. Pol a is a multisubunit enzyme, one subunit of which performs the primase function. Pol a 5 ->3 polymerase activity adds a short piece of DNA to the RNA primer. Pol 8 completes DNA synthesis on the leading strand and elongates each lagging strand fragment, using 3 ->5 exonuclease activity to proofread the newly synthesized DNA. Pol p and pol e are involved in carrying out DNA "repair," and pol y replicates mitochondrial DNA. 

There are many different types of DNA polymerases, and they vary greatly in their activities and in the nature of the reactions they catalyze. Some polymerases are involved mainly in the replication of DNA. Others are used for the repair of damaged DNA. There is also an important difference between the enzymes isolated from eukaryotes and those isolated from prokaryotes. Most of the eukaryotic DNA polymerases that have been isolated so far have just the simple 5 —> 3 polymerization activity shown in equation 14.1. Prokaryotic DNA polymerases, however, are multifunctional. In addition to their 5 — 3 polymerase activity, they possess a 3 5 exonuclease activity that can excise incorporated... 

TWn relatively recent developments have added to our knowledge significantly concerning how DNA replication occurs with fidelity or in what molecular biologists and biochemists call a processive polymerase activity. DNA polymerase is the enzyme which actually polymerizes (adds DNA precursors or building blocks) DNA. There are many such DNA polymerases in pro- and eukaryotic cells that have different functions but the main enzyme in prokaryotes is DNA polymerase 111 and in Eukaryotes. DNA polymerases alpha, delta, and epsilon. All four of these DNA polymerases are made of subunits. 

Mizushina Y, Ishidoh T, Kamisuki S, Nakazawa S, Takemura M, Sugawara F, Yoshida H, Sakaguchi K. 2003. Flavonoid glycoside A new inhibitor of eukaryotic DNA polymerase alpha and a new carrier for inhibitor-affinity chromatography. Biochem Biophys Res Com 301 480-487. 

Krishna, T. S., Kong, X. P., Gary, S., Burgers, P. M., and Kuriyan, J. 1994. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79 1233-1243. 

Known members of the family X polymerases include eukaryotic DNA polymerase [1 (pol fi) (Abbotts et al., 1988), polymerase a (Burgers et al, 2001), polymerase fi (Dominguez et al, 2000), polymerase X (Garcia-Diaz et al, 2000), yeast polymerase IV (Prasad et al, 1993), and the African swine fever virus polymerase X (Martins et al, 1994). Pol [1 is known to be involved in the base excision repair (BER) pathway, which is important for repairing... 

Physarum phospholipids (PHYLPA), isolated from myxoamoebae of Physarum polycephalum, is an inhibitor of eukaryotic DNA polymerase [71]. PHYLPA inhibits the proliferation of human fibroblasts cultured in a chemically defined medium. 

Know the roles of DNA polymerase I, II, III, and eukaryotic DNA polymerases, the roles of primers, helicases, single-stranded binding proteins (SSB), topoisomerases (gyrase), ligases, primase, and RNA polymerases, and the differences between the leading and lagging strands of DNA. 

DNA Damage Repair, Chemistry of Eukaryotic DNA Polymerases, Chemistry of Homologous Recombination Nucleic Acids, Enzymes that Modify... 

U. Hubscher, H.-P. Nasheuer, and J.E. Syvaoja. 2000. Eukaryotic DNA polymerases A growing family Trends Biochem. Sci. 25 143-147. (PubMed)... 

In eubacteria and eukaryotes, several types of DNA polymerases have been characterized three in eubacteria (DNA polymerases I, II and III), and five in eukaryotes (DNA polymerases a, 3, 6, e and )). Some of these enzymes, named DNA replicases , are specifically involved in DNA-chain elongation at the replication fork. They have a multi-subunit structure and can prime and perform DNA replication in a processive way when they are associated with the other replicative proteins. In eubacteria, only one DNA replicase has been isolated (DNA polymerase III), whereas several DNA replicases co-exist in eukaryotes DNA polymerases a, 6 and e, which are essential for the replication of nuclear DNA, and DNA polymerase y, which is responsible for the replication of the mitochondrial genome. The other eubacterial and eukaryotic DNA polymerases are monomeric and are preferentially involved in mechanisms which require replication of short DNA fragments, in the course of either DNA repair (DNA polymerases I and II from E. coli, eukaryotic DNA polymerase 3), or DNA replication (maturation of Okasaki fragments by E. coli DNA polymerase I). 

The two short stretches of amino-acid sequences of the DNA polymerase from P. furiosus which have been published were aligned with eukaryotic DNA polymerases of the B family to claim another eukaryotic feature of archaebacteria [137]. However, Fig. 11 shows that these amino-acid stretches of P. furiosus DNA polymerase and of other archaebacterial DNA polymerases align as well with E. coli DNA polymerase II, a prokaryotic member of the B family [138]. The presence of family B DNA polymerases in the three domains strongly suggests that the divergence between the DNA polymerases of families A, B and C occurred before the divergence between archaebacteria, eubacteria... 

An additional aphidicolin-resistant DNA polymerase composed of several 35 0 kDa polypeptides has been reported in S. acidocaldarius [146] and in T. acidophilum [ 41]. The authors have proposed that this DNA polymerase could be homologous to the eukaryotic DNA polymerase (3, which is a monomeric enzyme composed of a 40 kDa polypeptide. However, we have shown that in each case, the 35-40 kDa polypeptides are devoid of DNA polymerase activity when they are totally separated from the high-molecular-mass DNA polymerase already described[141,142],... 

In the halophile H. halobium, Nakayama et al. [148] have described an aphidicolin-sensitive DNA polymerase that they named DNA polymerase a . The enzyme has a high sedimentation coefficient value, is able to synthesize RNA on a synthetic DNA template, and is associated with a 3 to 5 exonuclease activity. Two major polypeptides of 60 and 70kDa were detected in a purified fraction of H. halobium DNA polymerase a [149]. The authors concluded from these results that this enzyme corresponds to a multi-subunit DNA polymerase able to perform DNA priming like eukaryotic DNA polymerase a. However, the association of the 60 and 70 kDa polypeptides with the polymerase activity has not been demonstrated and the specific activity of the enzyme is very low compared to any other purified DNA polymerases. 

Hiibscher U, Maga G, Spadari S (2002) Eukaryotic DNA polymerases. Annu Rev Biochem 71 133-163... 

Eukaryotic DNA polymerases have also been isolated and characterized as listed in Table 22.1. Based on studies of SV40 DNA replication in vitro, it has been found that DNA polymerase d has high processivity and is required for leading-strand synthesis, making it analogous to E. coli DNA pol III. DNA polymerase d requires ATP and is stimulated by two additional DNA replication proteins, RF-C and PCNA. DNA polymerase a serves the same role as E. coli DNA pol I in that DNA polymerase a is necessary for lagging-strand synthesis. In addition to DNA polymerase a and d, three other DNA polymerizing activities have been identified. DNA polymerase I is involved in DNA repair and is most similar to E. coli DNA pol II. DNA polymerase b is also a repair enzyme, and DNA polymerase g is required for mitochondrial DNA synthesis. 

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