Polymerase Nomenclature 1

Eur. J. Biochem. 191, 617-618 (1990) FEBS 1990

Revised nomenclature for eukaryotic DNA polymerases Peter M. J. BURGERS’, Robert A. BAMBARA’, Judith L. CAMPBELL3, Lucy M. S. CHANC4, Kathleen M. DOWNEY’. Ulrich HUBSCHER6, Marietta Y. W. T. LEE’, Stuart M. LINN7, Antero G. SO5 and Silvio SPADAR16 Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, USA Department of Biochemistry, University of Rochester, Rochester, USA Department of Chemistry, California Institute of Technology, Pasadena, USA Department of Biochemistry, Uniformed Services University Health Sciences, Bethesda, USA Department of Medicine, University of Miami School of Medicine, Miami, USA Institut fur Pharmakologie und Biochemie, Universitit Zurich-Irchel, Zurich, Switzerland ’ Department of Biochemistry, University of California, Berkeley, USA (Received December 18, 1989) - EJB 89 1505

In 1975, a Greek letter nomenclature system was adopted for the DNA polymerases from higher eukaryotes [I]. This nomenclature defined DNA polymerases a, and y . The recent isolation and characterization of at least two new classes of DNA polymerases, collectively called DNA polymerase 6, has led to some confusion, even among researchers in this field. In addition, there has been a growing appreciation of a strong analogy between the yeast Saccharomyces cerevisiae and mammalian systems with regard to the enzymology of DNA replication. In yeast, however, the DNA polymerases have traditionally been identified by Roman numerals. Thus, at the recent Conference on Eukaryotic DNA Replication in Cold Spring Harbor (30 August - 3 September, 1989), scientists active in this field discussed a revision of the current nomenclature. It was decided to (a) adopt the Greek letter nomenclature for the yeast DNA polymerases, and (b) use the close correlation between many of the mammalian and yeast enzymes in conjunction with the known primary structures of all but one of the yeast enzymes to further classify the mammalian DNA polymerases. This classification is listed in Table 1. DNA polymerases a, p and y have been reviewed comprehensively [2]. In brief, DNA polymerase CI in a complex with DNA primase is a replicative DNA polymerase. The primary structures of the human and yeast catalytic polymerase polypeptides, as deduced from the gene sequence, show a high degree of similarity [5, 61. DNA polymerase j?,not found in yeast to date [7], is the only small DNA polymerase isolated so far. DNA polymerase y is a nuclear-encoded DNA polymerase found in the mitochondria. The primary structure of the yeast form shows that homology with other classes of DNA polymerases is limited [8]. In yeast the enzyme is required for mitochondrial, but not for nuclear DNA replication [8]. In 1976 a novel DNA polymerase was isolated from rabbit reticulocytes [lo]. This enzyme was originally distinguished from DNA polymerase a by its proofreading 3’-5’ exonuclease activity and was namend DNA polymerase 6. Recently, a number of additional mammalian DNA polymerases

Correspondence to P. Burgers, Dept of Biochemistry and Molccular Biophysics, Washington University School of‘ Medicine, St. Louis, MO 63110, USA Abbreviution. PCNA, proliferating all nuclear antigen.

Table 1 . Eukaryotic D N A polyrnerases Numbers in parcnthescs are the molccular masses (kDa) of the catalytic polypeptides; m, mitochondria DNA polymerase

Yeast enzyme

2

I

P

-

(167)

m (147) I11 (125) IT (170)

Y

6 c

Yeast gene

Mammalian designation

Reference

POLI” MZPl POZJb

z (165)

B (39)

5, 6 22 8 9, 12 15-18,21

-

7

6, h 1 (125) 6, 62, 611 (140 - 21 5)

~~

a

~

Former gene designation, CDCl7 Former gene designation, CDC2.

have been isolated, which have all been named DNA polymerase 6 because of the presence of a proofreading 3’-5’ exonuclease. Structural and biochemical evidence, however, suggests that these enzymes fall in at least two groups. The knowledge, that in yeast the two &like DNA polymerases are also distinct on genetic grounds, prompted us to propose the following classification. (a) DNA polymerase 6 is involved in a nuclear DNA replication (reviewed in [3, 111). For a high processivity (i.e. a tendency of the DNA polymerase to remain bound to the DNA through successive polymerization cycles) on model homopolymer templates containing long single-stranded regions between primers, this enzyme requires as a cofactor proliferating cell nuclear antigen (PCNA). The calf thymus polymerase 6 studied by So and Downey [3] and yeast DNA polymerase 111 studied by Burgers [4] are two representative enzymes in this class [12, 131. For both enzymes, the size of the catalytic polymerase polypeptide is 125 kDa. DNA polymerase 6 is required for in vitro Simian virus 40 DNA replication and mutations in the ycast gene POL3 (formerly CDC2) encoding the polymerase polypeptide show a defect in replicative DNA synthesis (reviewed in [4, 111). (b) DNA polymerase c. Yeast DNA polymerase I1 has been shown by studies with appropriate mutants to be distinct from cc(I), y(mitochondrial), and G(II1) [9, 141. It, like DNA polymerase 6, has a proofreading exonuclease activity, but is processive in the absence of PCNA [4]. The analogous mammalian enzymes have until now been identified as DNA polymerase h2 or 6,, or PCNA-independent 6. These include

61 8 the enzyme from calf thymus from Hiibscher’s group [15] and from Bambara’s group (Pol hII) [16], the enzyme from HeLa cells from Linn’s group (Pol 6,) [17], and the enzyme from human placenta from Lee’s group [18]. DNA polymerase G isolated from HeLa cells is most likely involved in DNA repair [17]. All of these enzymes are processive and are only marginally, if at all, stimulated by PCNA. A DNA polymerase isolated from rabbit bone marrow by Byrnes et al. may also fall in this class [19]. This classification is not complete and can certainly not be completed until the genes for these enzymes have been isolated and the precise appropriate structural and functional comparisons can be made. Thus, as a cautionary note, the enzymes grouped together under DNA polymerase F show a large variation in the size of the catalytic polypeptide (140215 kDa), which may reflect proteolytic degradation and posttranslational modification, but also the presence of genetically distinct species. Further, this classification does not include certain additional classes of DNA polymerases such as (a) the plant chloroplast DNA polymerase, and (b) a yeast DNA polymerase predicted by the sequence of the REV3 gene, but for which no enzymatic activity has yet been demonstrated [20]. This putative DNA polymerase appears to be involved in mutagenic DNA repair. In conclusion, we favor the approach of using a separate letter of the Greek alphabet to designate each genetically distinct DNA polymerase. REFERENCES 1 a. Weissbach, A,, Baltimore, D., Bollum, F., Gallo, R . & Korn, D. (1975) Science 190, 401 -402. 1 b. Weissbach, A,, Baltimore, D., Bollum, F., Gallo, R. & Korn, D. (1975) Eur. J . Biochem. 59, 1-2. 2. Fry, M. & Loeb, L. A. (1986) AnimalcellDNApolymerases, CRC Press, Boca Raton, FL.

3. So, A . G . & Downey, K . M. (1988) Biochemistry 27,4591 -4595. 4. Burgers, P. M. J. (3989) Prog. Nucleic Acids Res. Mol. Biol. 37, 235 - 280. 5. Wong, S. W , Wahl, A. F., Yuan, P. M., Arai, N., Pearson, B. E., Arai, K., Korn, D., Hunkapiller, M. W. & Wang, T. S. F. (1988) EMBO J . 7, 37-47. 6. Pizzagalli, A,, Valsasnini, P., Plevani, P. & Lucchini, G. (1988) Proc. Natl Acad. Sci. U S A 85, 3772-3776. 7. Chang, L. M. S. (1976) Science 191, 1183-1185. 8. Foury, F. (1989) J . Biol. Chem. 264,20552-20560. 9. Boulet, A., Simon, M., Faye, G., Bauer, G. A. & Burgers, P. M. J. (1989) EMBO J . 8 , 1849-1854. 10. Byrnes, J. J., Downey, K . M., Black, V. L. & So, A. G. (1976) Biochemistry 15, 2817-2823. 11. Blow, J. J. (1989) TrendsGenet. 5, 134-136. 3 2. Lee, M. Y. W. T., Tan, C. K., Downey, K . M. & So, A. G. (1984) Biochemistry 23, 1906-1913. 13. Bauer, G . A., Heller, H. M. & Burgers, P. M. J. (1988) J . Bid. Clzem. 263, 917-924. 14. Sitney, K . C., Budd, M. E. & Campbell, J . L. (1989) Cell 56, 599 - 605. 15. Focher, F., Spadari, S., Ginelli, B., Hottiger, M., Gassman, M . & Hiibscher, U. (1988) Nucleic Acids Res. 16, 6279-6295. 16. Wahl, A. F., Crute, J. J., Sabatino, R. D., Bodner, J. B., Marraccino, R. L., Harwell, L. W., Lord, E. M. & Bambara, R. A. (1986) Biochemistry 25, 7821 -7827. 17. Syvaoja, J . & Linn, S. (1989) J . Biol. Chem. 264, 2489-2497. 18. Lee, M. Y. W. T. &Toomey, N . L. (1987) Biochemistry26,10761085. 29. Goscin, L. P. & Byrnes, J. J . (1982) Biochemistry 21, 2513. 20. Morrison, A , , Christensen, R. B., Alley, J., Beck, A. K., Bernstine, E. G., Lemontt, J. F. & Lawrence, C. W. (1989) .J. Bacteriol. 171, 5659 - 5667. 21. Budd, M. E., Sitney, K. C. &Campbell, J. L. (1989) J . Biol. Chem. 264,6557-6565. 22. Matsukage, A., Nishikawa, K., Ooi, T., Seto, Y. & Ydmaguchi, M. (1987) J . Biol. Chem. 262, 8960-8962.