k.=)
1991
Oxford University Press
Nucleic Acids Research, Vol. 19, No. 15 4045-4057
Compilation and alignment of DNA polymerase
sequences
Junetsu Ito and Dan K.Braithwaite Department of Microbiology and Immunology, College of Medicine, University of Arizona Health Sciences Center, Tucson, AZ 85724, USA Received May 29, 1991; Revised and Accepted July 9, 1991
INTRODUCTION More than 40 different DNA polymerases, including some putative DNA polymerase sequences deduced from nucleotide sequence data, have recently been reported (1-39). The amino acid sequences of these DNA polymerases have been aligned and partial homologous regions identified by many investigators (2-4,9,10,12-25,27-36,42-51). Based on the segmental amino acid sequence similarities, DNA polymerases have been classified into two major groups; E. coli DNA polymerase I-Type and eukaryotic DNA polymerase ca-Type (14,44,47,48,51), or family A DNA polymerases and family B DNA polymerases (4,9,50). As the number of DNA polymerase sequences increases, the classification of DNA polymerases becomes increasingly ambiguous. For example, DNA polymerase delta of yeast was shown to have amino acid sequence similarity to the a-Type DNA polymerases (17). It has become necessary to establish a unified classification of DNA polymerases. Here we propose to classify DNA polymerases into families A, B, and C (Figure 1: A, B, and C), according to the amino acid sequence homologies with E. coli DNA polymerases I, II, and III, respectively. As new and different prokaryotic and eukaryotic DNA polymerases are identified, the number of families can easily be expanded by using additional letters of the alphabet (i.e., D, E, etc.). The bacterium E. coli (strain K12) contains three distinct DNA polymerases I, II, and HI (52). E. coli DNA polymerase I, the first DNA polymerase discovered, is specified by the polA gene (52). E. coli DNA polymerase II, encoded by the polB gene, was recently sequenced and found to be identical to the dinA gene, a DNA damage inducible gene whose expression is regulated by the SOS system in E. coli (8,53). Amino acid sequence alignment shows that E. coli DNA polymerase II has significant homology with family B (a-Type) DNA polymerases (8,53,54). E. coli DNA polymerase IH is a multisubunit enzyme encoded by various dna genes (55); the DNA polymerizing a-subunit encoded by the polC (dnaE) gene (56) and the 3'- 5' exonuclease performing e-subunit encoded by the dnaQ gene (57). The asubunit of E. coli DNA polymerase III exhibits an extensive homology with the corresponding a-subunit of Salmonella typhimurium DNA polymerase m (35); and both show significant homology to Bacillus subtilis DNA polymerase HI, a singlepolypeptide encoded by the polC gene (36). In summary, family A DNA polymerases are named for their homology to the product of the polA gene encoding E. coli DNA polymerase I; family B DNA polymerases are named for their
homology to the product of the polB gene encoding E. coli DNA polymerase 11; and family C DNA polymerases are named for their homology to the product of the polC gene encoding E. coli DNA polymerase HI. The eukaryotic DNA polymerase (3, the smallest known DNA polymerase, does not have homology with those of any of the DNA polymerase families described above. Instead, DNA polymerase (3 has homology with terminal transferases (37). This ,B group we will call family X (Figure ID). The classification and original reference(s) for the amino acid sequences of each DNA polymerase are shown in Table 1. All of the family A DNA polymerases, except for yeast mitochondrial DNA polymerase I, are prokaryotic and are very sensitive to dideoxynucleotide inhibitors, and therefore are useful enzymes for DNA sequencing by the chain-termination method (58). The family A DNA polymerases are resistant to aphidicolin. The family B DNA polymerases are quite extensive in number and variety. Most of the family B DNA polymerases, if not all, are sensitive to aphidicolin and relatively resistant to dideoxynucleotide inhibitors. Most of the family B DNA polymerases, except for pAI2 (33) and yeast DNA polymerase II (16), contain the highly conserved amino acid sequence motif YGDTD, which has been suggested to form part of the dNTP binding site. Amino acid substitutions in this conserved sequence resulted in defects in the DNA polymerase activity without affecting the 3'- 5' exonuclease activity (59,60,61). The family C DNA polymerases are major bacterial replicative DNA polymerases which do not have appreciable homology with those of family A and B DNA polymerases. B. subtilis DNA polymerase Im is a single polypeptide that is highly sensitive to hydroxyphenylazouracil (62). It is anticipated that the number of sequenced family C DNA polymerases will increase rapidly, since all of the aerobic bacteria may contain a member of this family of DNA polymerases.
SEQUENCE ALIGNMENT The 37 complete DNA polymerase sequences and 3 complete terminal deoxynucleotidyltransferase (TDT) sequences are listed in 4 groups; the family A DNA polymerases, the family B DNA polymerases, the family C DNA polymerases, and family X DNA polymerases (including TDTs). In order to limit the space needed for the alignment, we omitted DNA polymerase sequences that are very similar to the prototype DNA polymerase. The DNA polymerases not shown include: herpes virus type-2 (63),
4046 Nucleic Acids Research, Vol. 19, No. 15 adenovius Wpe-S (64), bacteriophage T3 (65), and bacteriophage PZA (66).
ACCURACY OF SEQUENCE DATA Whenever a sequence ambiguity existed in a published sequence, we contacted the authors to obtain the updated sequence a few publisd amino acid sequences information. We found differ at one or more positions from their GenBank/EMBL entry. Again, we have communicated with the primary author to confirm the correct sequences. The multiple alignment of the amino acid sequences was obained by a series of pairwise aligments combined and adjusted by eye into larger and larger subsets of similar sequences. The process of combining and adjusting by eye was aided by modified versions of the MOTIF program (67) and the ALIGN program (68). The GAP and BESTFIT programs, from UWGCG (University of Wisconsin Genetic Computer Group) (69), initay generated the pairwise alignments, adjusted for maximum alignment that allowed for a considerable number of gaps. We then compressed these alignments by eye to give a more contiguous alignment. The alignment of the sequences for optimal similarity is straightforward in the areas of relatively conserved strucure, but is much more arbitary in the more varied sequence areas. The alignment of the varied areas should therefore be regarded as less than optimal in view of the difficulties concerned with multiple alignments in these areas. Finally, we invite fiuther correction from readers, and welcome suggested revisions and altemative alignments.
ACKNOWLEDGEMENTS This work was supported by grant GM28013 from the National Institutes of Health and by grant NP-704 from the American Cancer Society.
REFERENCES 1. Joyce, C.M., Kelley, W.S. and Grindley N.D.F. (1982) J. Biol. Chem. 257, 1958-1964. 2. Lopez, P., Martinez, S., Diaz, A., Espinosa, M. and Lacks, S.A. (1989) J. Bio. Chem. 264, 4255-4263. 3. Lawyer, F.C., Stoffel, S., Saiki, R.K., Myambo, K., Dnmmond, R. and Gelfand, D.H. (1989) J. BRil. Chem. 264, 6427-6437. 4. Leavitt, M.C. and Ito, J. (1989) Proc. NatL. Acad. Sci. U.S.A. 86, 4465-4469.
5. Dunn, J.J. and Stuiier, F.W. (1983) J. Mol. Biol. 166, 477-535.
6. RAdn, B. and Rutberg, L. (1984) J. Virol. 52, 9-15. 7. Foury, F. (1989) J. Biol. Ceem 264, 20552-20560. 8. Iwasaki, H., Ishino, Y., Toh, H., Nakata, A. and Shinagawa, H. (1991)
Mol. Gen. Genet. 226, 24-33. 9. Jung, G., Leavitt, M.C., Hsieh, J.-C. and Ito, J. (1987) Proc. Natt. Acad. Sd. U.S.A. 84, 8287-8291. 10. Savilahti, H. and Bamford D.H. (1987) Gene 57, 121-130. 11. Yoshikawa, H. and Ito, J. (1982) Gene 17, 323-335. 12. Matsumoto, K., Takano, H., Kim, C.I. and Hirokawa, H. (1989) Gene 84, 247-255. 13. Spicer, E.K., Rush, J., Fung, C., Reha-Krantz, L.J., Karam, J.D. and Konigsberg, W.H. (1988) J. Biol Chem. 263, 7478-7486. 14. Wong, S.W., Wahl, A.F., Yuan, P.-M., Arai, N., Pearson, B.E., Arai, K.-i., Korn, D., Hunkapiller, M.W. and Wang, T.S.-F. (1988) EMBO J. 7, 37-47. 15. Pizzagalli, A., Valsasnini, P., Plevani, P. and Lucchini, G. (1988) Proc. Natl. Acad. Sd. U.S.A. 85, 3772-3776. 16. Morison, A., Arad, H., Clark, A.B., Hamatake, R.K. and Sugino, A. (1990) Cell 62, 1143-1151.
17. Boulet, A., Simon, M., Faye, G., Bauer, G.A. and Burgers, P.M.J. (1989) EMBO J. 8, 1849-1854. 18. Morrison, A., Christensen, R.B., Alley, J., Beck, A.K., Bernstine, E.G., Lemontt, J.F. and Lawrence, C.W. (1989) J. Bacteriol. 171, 5659-5667. 19. Gibbs, J.S., Chiou, H.C., Hall, J.D., Mount, D.W., Retondo, M.J., Weller, S.K. and Coen, D.M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 7969-7973. 20. Kouzarides, T., Bankier, A.T., Satchwell, S.C., Weston, K., Tomlinson, P. and Barrell, B.G. (1987) J. Virol. 61, 125-133. 21. Baer, R., Bankier, A.T., Biggin, M.D., Deininger, P.L., Farrell, P.J., Gibson, T.J., Hatfull, G., Hudson, G.S., Satchwell, S.C., S6guin, C., Tuffnell, P.S. and Barrell, B.G. (1984) Nature 310, 207-211. 22. Davison, A.J. and Scott, J.E. (1986) J. Gen. Virol. 67, 1759-1816. 23. Binns, M.M., Stenzler, L., Tomley, F.M., Campbell, J. and Boursnell, M.E.G. (1987) Nucl. Acids Res. 15, 6563-6573. 24. Earl, P.L., Jones, E.V. and Moss, B. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3659-3663. 25. Tomalski, M.D., Wu, J. and Miller, L.K. (1988) Virology 167, 591-600. 26. Gingeras, T.R., Sciaky, D., Gelinas, R.E., Bing-Dong, J., Yen, C.E., Kelly, M.M., Bullock, P.A., Parsons, B.L., O'Neill, K.E. and Roberts, R.J. (1982) J. Biol. Chem. 257, 13475-13491. 27. Engler, J.A., Hoppe, M.S. and van Bree, M.P. (1983) Gene 21, 145-159. 28. Shu, L., Hong, J.S., Wei, Y.-f. and Engler, J.A. (1986) Gene 46, 187-195. 29. Paillard, M., Sederoff, R.R. and Levings, C.S. miI (1985) EMBO J. 4, 1125-1128. 30. Stark, M.J.R., Mileham, A.J., Romanos, M.A. and Boyd, A. (1984) Nucl. Acids Res. 12, 6011-6030. 31. Tommasino, M., Ricci, S. and Galeotti, C.L. (1988) Nucleic Acids Res. 16, 5863-5878. 32. Oeser, B. and Tudzynski, P. (1989) Mot. Gen. Genet. 217, 132-140. 33. Kempken, F., Meinhardt, F. and Esser, K. (1989) Mol. Gen. Genet. 218, 523-530. 34. Tomasiewicz, H.G. and McHenry, C.S. (1987) J. Bacteriol. 169, 5735-5744. 35. Lancy, E.D., Lifsics, M.R., Munson, P. and Maurer, R. (1989) J. Bacteriol. 171, 5581-5586. 36. Hammond, R.A., Barnes, M.H., Mack, S.L., Mitchener, J.A. and Brown, N.C. (1991) Gene 98, 29-36. 37. Mashge, A., Nishikawa, K., Ooi, T., Seto, Y. and Yamaguchi, M. (1987) J. Biol. Chem. 262, 8960-8962. 38. Abbotts, J., SenGupta, D.N., Zmudzka, B., Widen, S.G., Notario, V. and Wilson, S.H. (1988) Biochemistry 27, 901-909. 39. SenGupta, D.N., Zmudzka, B.Z., Kumar, P., Cobianchi, F., Skowronski, J. and Wilson, S.H. (1986) Biochem. Biophys. Res. Com 136, 341-347. 40. Peterson, R.C., Cheung, L.C., Mataliano, R.J., White, S.T., Chang, L.M.S. and Bollum F.J. (1985) J. Biol. Chen. 260, 10495-19502. 41. Koiwai, O., Yokota, T., Kageyama, T., Hirose, T., Yoshida, S. and And, K.-i. (1986) Nulc. Acids Res. 14, 5777-5792. 42. Argos, P., Tucker, A.D. and Phillipson, L. (1986) Virology 149, 208-216. 43. Larder, B.A., Kemp, S.D. and Darby, G. (1987) EMBO J. 6, 160-175. 44. Hall, J.D. (1988) Trends Genet. 4, 42-46. 45. Reha-Krantz, L.J. (1988) J. Mol. Biol. 202, 711-724. 46. Bemad, A., Zaballos, A., Salas, M. and Blanco, L. (1987) EMBO J. 6, 4219-4225. 47. Wang, T.S.-F., Wong, S.W. and Kom, D. (1989) FASEB 3, 14-21. 48. Bernad, A., Blanco, L., Lazaro, J.M., Martin, G. and Salas, M. (1989) Cell 59, 219-228. 49. Polesky, A.H., Steitz, T.A., Grindley, N.D.F. and Joyce, C.M. (1990) J. Biol. Chem. 24, 14579-14591. 50. Ito, J. and Braithwaite, D.K. (1990) Nucl. Acids Res. 18, 6716. 51. Blanco, L., Bernad, A. and Salas, M. (1991) Nucl. Acids Res. 19, 955. 52. Kornberg, A. (1974) DNA replication. W.H. Freeman and Co., San Francisco. 53. Bonner, C.A., Hays, S., McEntee, K. and Goodman M.F. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 7663-7667. 54. Chen, H., Lawrence, C.B., Bryan, S.K. and Moses, R.E. (1990) Nucl. Acids Res. 18, 7185-7186. 55. McHenry, C.S.(1985) Mol. Cell. Biochem 66, 71-85. 56. Shepard, D., Oberfelder, R.W., Welch, M.W. and McHenry, C.S. (1984) J. Bacteriol. 158, 455-459. 57. Scheuerman, R., Tam, S., Burgers, P.M.J., Lu, C. and Echols, H. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 7085-7089. 58. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467. 59. Dorsky, D.I. and Crumpacker, C.S. (1990) J. Virol. 64, 1394-1397. 60. Bemad, A., Lizaro, J.M., Sles, M. and Blano, L. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4610-4614.
Nucleic Acids Research, Vol. 19, No. 15 4047 61. Jung, G., Leavitt, M.C., Schultz, M. and Ito, J. (1990) Biochem. Biophys. Res. Comm. 170, 1294-1300. 62. Neville, M.N. and Brown, N.C. (1972) Nature New Biol. 240, 80-82. 63. Tsurumi, T., Maeno, K. and Nishiyama, Y. (1987) Gene 52, 129-137. 64. Dekker, B.M.M. and Van Ormondt, H. (1984) Gene 27, 115-120. 65. Beck, P.J., Gonzalez, S., Ward, C.L. and Molineux, I.J. (1989) J. Mol. Biol. 210, 687-701. 66. Paces, V., Vlcek, C., Urbanek, P. and Hostomsky, Z. (1985) Gene 38, 45-56. 67. Smith, H.O., Annau, T.M. and Chandrasegaran, S. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 826-830. 68. Doolittle, R.F.and Feng, D.-F. (1990) In Doolittle, R.F. (ed.), Methods in Enzymol. -Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences. Academic Press, New York, Vol. 183, pp. 659-669. 69. Devereux, J., Haeberli, P. and Smithies, 0. (1984) Nucl. Acids Res. 12, 387-395.
Classification of DNA polymerases A.
Family A DNA po e 1.
Bacteral DNA p a) b) c)
2.
References
c ca DNA poiynmrasc I
S&Wwcccus p_m cniae DNA polymerase Themr
I
aquadcu DNA polymerase I
TS DNA polymerase 17 DNA polymerase Spo2 DNA polymerase
(7)
Family B DNA pom 1.
Bacterial DNA pobm E- ci DNA polymerase II
2.
PRDI DNA polymerase5 #29 DNA p merase M2 DNA polymerase T4 DNA p rase
3.
Ekarysodc DNA polymeaes
4.
Human DNA polymerase alpha Yeast DNA polymerase I Yeast DNA polmeras II Yeast DNA poymerase HI (delta) Yeast DNA polymerase Rev3 Viral DNA polymases a) b) c) d) e)
a) b) c) d) e) f)
g) h) i) j) S.
(8)
Bacteriophage DNA polymera
a) b) c) d)
Herpes-1 DNA polymerase Human cytomeplovirus DNA polymerase Epstein-Barr virus DNA polymerase Variceila-Zoster virus DNA polymerase Fowlpox virus DNA polymerase Vaccinia virus DNA polymerase Autographa californica nuclear polyedrosis virus (AcMNPV) DNA polymerase Adenovrus-2 DNA polymerase Adenovirus-7 DNA polymerasel Adenovirus-12 DNA polymerase*
(9,10) (11) (12) (13)
(14)
(15)
(16) (17) (18)
(19) (20) (21) (22) (23) (24) (25) (26)
(27)
(28)
Eukaryotic linear DNA plasmid encoded DNA polymerases a) b) c) d) e)
C
(4) (5) (6)
Mltocho l DNA p merase Yeast mitochondrial DNA polymerase (MIPI)
B.
(1) (2) (3)
Bacteriophage DNA pomerases a) b) c)
3.
ase
S-1 maize mitochondrial DNA polymerase es lacdis plasmid pGKLI DNA polymerase Kyveryces lacts plasmid pGKI2 DNA polymerase Claicep pwpura plasmid pCLKU DNA polymerase Ascobolu unmeu plasmid pAI2 DNA polymerase
Kkqyvw
(29) (30) (31) (32)
(33)
Family C DNA polymerases Bacterial replicative DNA polymerases
a) b) c) D.
E coi DNA polymerase III a subunit Sabnonel yphmwiwu DNA polymerase III a subunit Bacius subi DNA polymerase I
Family X DNA p a) b) c) d) e)
(34) (35)
(36)
a
Rat DNA polymerase ^ Human DNA polymerase 8 Human terminal deaxynucleotidyltransferase (TdT) Bovine terminal deaoynucleotidyltransferase (TdT) Mouse terminal deoxynud1eotiltransferase (dT)
(37) (38,39) (40) (41) (41)
Table 1. The main families and subclassifications of DNA polymerases. Those DNA polymerases marked with a star (*) are protein-primed DNA polymerases.
4048 Nucleic Acids Research, Vol. 19, No. 15 e.Ao
O 0
t%9o
V%0..-40400-.-
0
.N0,1
0o M"D
0o C
CCb.*-GOp
C
018,14rm
0
z
0'Oui0
60
0
v
U
,''''''Yb4. m
99
129-
9-
.199* a
...JbU
1
3
.
Me9~~9
:
0 *.w.. 3b1...b 0u.8..au..
_j
Zli
0
3.. > * * v v v v * @
Ben
w.- .w.
g.
&4-Yb..
J
-a..
, ~~~~~~~~~~~~~~~~~~3 I::
4~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~11 ~ ~ ~ ~ ~ ~ ~ 01. C-Ybb0
b-Yb .L.. so
P.-j.X -o11
.
J
acs
-b
Ez
Of-cafb-Y06
.216a :.J.64:-a.. Jj: 3W -ic wltl*wa
3~~~~!OBS:
:o**v@*0 r2
,
Sb~~~mw
.-11
IZ *
w§
*lu
.J=.
Yb'V'O'
1~2
t
.
@.19..I
.
.
.3
Yb
.
W.*9b
.19. WW
.J 'Ybb
-
J-'.
9.3.Y
J9
W-.5.b 9
_J.J_:j:e
3
.339
@@ :.Z
*@*@
u
*XX
.1W095.3.Yb
..'9bb* b-bLY0b
'
oftf.Yb''''5
V644
~
...Sb.
00az0* 2SI.aea
b-
:IL
-.934 U.5.o . WYbYb 0 ..Yb..3b ..Zs.3 .3...~~~~~~~~~~~~~~~~~9 .J~~~I . b----rd 0~~ :~~~~~~~~~~~~~J395.31
Ii
10
Ybb-0.
.....Yb.
"''"s:
19
~~:::
0 _ Te-3 VW.ISISYb4R:~~~~~~~~~~~a.01
.b made9..9.
~~~Z!8.-*~~~~~~~~~~.
.539.
.
.
Us.
5w53 :::~
~~~~~~~ ..~c- .3 .b .J.. .M :* .w . . v
' . 5YLC.S ::: Yb..0.' 0953 ....4..ie~~~~~~~~~~~~660 YbtY ..b .R -. *9.bYIb6
fMb
r-
PLe..W.J'.99OW.JO.Cq
:
3:
-
00 3
0
. .~..J99 . . Z=QE
*-@
@
co
b
0.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~5-
~w
I
**-:*:T:
: JYwI..=-.JU. e ::;::: .AC,
$..Wu#
''''' .3
*~ ~ ~ ~ ~ ~''''''3'
q
.3.
:* MUIIA
z
_.9.. ''''''9-e Yb * | * * -< ''*
-JO
3-
P. Yb.C
t
:* a.ss ICIZ
416.J30
3
:W:~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~e
95~~~~~~
...
6
.
z
0..
:-9.
la 0 ~~~::~~~g: :~~~~-~''~~~ 0.-C., ....19..b-~M6 9 Y19950950 3.9-. l..J b--M" M I . Y. -U.5b3 :: ---bI Le 019S1.9b--
03
''-I
0 3W ..9'. bY-zb J-~~~49bYbbb bI 4LYb4.. . ''S'9 Yb bbbbJJ .de0j.....J4 000~~~.b* b- :..O 4--b9.. W,5--J. *
v% >_> im
222J
:.JYb Yb.S'..Qft
4494 Yb44W
.
Ls.
w
.I. mm -da
B
*v "Yb
4L.~~~~~~~~~~~~~~1 .Jb--.
*
*b-02
*
-- i Y4f.Jb5 '"'2.JJJJ-bYb..bb995 AL~~~~~~~~~~~
.Jl9..Ji
.J'''Yb* Wu~~~~~~~~~~~~~~~~3 8L.-.WILM
44b-
YbYb_3
S
9590
AZ _.Jj
.Jb..9J.-
''6b-0Yb.J9Yb b'=.J-
'.W3.0
J 1''.
3U~~:::J: :1 :,-L W -3-
0h9Y. :~: wfat WH
YbCb8b 9 ..o ~ b--bb-3.J4094
:
33_bYb3YY
)
43W0
.J995..-
:
-C
;; 2
'E .1
::*-,IC
UseYb O. 33333
1539
00.YY 'Yb-Yb'a
0
..
0
s300
0b-YYb.a. 000.3
.j..j...js::I:W MCN8 `H :' b-40.0 3.p
-09.JIL
9'OV9N.-
-
#3~~~
3
C-b-Yb00YbYb. 0so M33 LWQ..II,el '0..e OWN
s
AL
_
b.' '06U.
3Y95bJ'**
''3
.
az
tg*
a..a
YbYbb'
W
.di
jcc) oA
_
I
Cz.* silo-
YbY b*-
0
1.11.9-b8.21 ~ b-b-
b-b- 8.2'
9
9-9-82'
V9 -9-82
YbZg ~* YbWm Yz 9~"I
~~ Yb2E~g~* .9
9
Uft~~~~~~~~JL
9
bb-
~
:S19
8C2' t Yb )-,
Nucleic Acids Research, Vol. 19, No. 15 4049 . t-M [email protected] 40
9-~~~~~i ~ ~ CO' : . . .. .090. .N) :
a
51:8 ::s16z .2 B0 :
:
-J..0
I
IC b. R 21I9"'10I 9-. ~
Aj2
0
U1.
23OX ...
0 39-429909 .99U
a W% b
. .~9.9 . ....
*'~~~'9-20~~~~~0. > 0 9~~~~~~~~~~.
.
~~~~~09.J>09 . .. ...
0
9,> >,
.
..
a 5- .5,,g .04MM
0.. 0.09.5. 09... W.
'IliI I0I00.
9096 "9-.>
5i. 5
9-9 .
u 0=90 Sa .a5099.6 ..-j
.
-
:IU6
_
6~9
.OL
c
:dLdLfx
_
9-
U09
209099.9-il.
929RJ
20-' 092094
.
9:L
09~~~~~~~~__j09 6_J .L.jjW
IUAW -ldC
9404a
O.-
..oi9 .0908ou.0 L E N.9
.N.j
W9 UWO%9 au
9-
:I-j~~~ a
J
40 409-
9
00
.09..J~~~09. 0 . .= to2
.. .09..i
. ..
.092092..~E.003 ::
.p.09.
..mI;-.M.. .s ~~~~~~-.~~~~~~~~~09 .
.h *2 0109 99-3
:8~~~~ul2ge3:: a
"I0
:
:
:§ 09
u -
in N
I
e
'-V
4
I
C&~9.
"& U'99
"1*9I~
II»ow>-.t&.,&a!)0 4
~~~~~~~:.6..1
9
USa u9.
4050 Nucleic Acids Research, Vol. 19, No. 15 ,;v O--o-NtOM
Go
C44cu-plgDa -C%IA;"=-4r-.0,00P.40"lnM= 4or-*;::9:8s ---
.
zuw_o=n
_s
zzw .
.
V33~~~~~ .o~ ." i.y .> . . .F< .
se***,. .. .. . . .iC
..2 .
.
IM
-MU-.*
** ~~ ~ ~J@ ~ * ~ *__~~~~ xa
~~~
.
.
. ..
*
.
*
.
O
*
t*
bd
@
sc
~ @@ed** J **** U.
*_ *@** *_U* M6o*
.~~~~~C . = tAV*rr_x
**.Z. ffi=:|72,ip * * *sOsy@iEg . . . .a
IW
ya.... :=>la *B*YYYyw~t * @ t >0..@-
* @** J_J
* @@ttW_z
. . v^ w
@
>||D-* --
_>
L
z
*qF
*
*-
-^la @
_
_
*@ @@""
W
* .....
cp-OYFo
---A-MUMS
9--
0
7= A>0 . rL ,.L- =3= z,9W,-6-0.0.4irIfi.-VI-i -
-
>-
c
-
--
9s
I
: .0 H :
,
U;
41 -1
. @ * s@
.. . . . . Fy
Nucleic Acids Research, Vol. 19,
0---*-O,-,Ol ;iz:!a O-t-w,oln
---o-o--=aN S'..
O-. 0
Ca 0NIN-0O 00
M OOCM
rowr owrl NNEJuu -
1............
cl ........... .....................|| w*3 * @ e e e e
o
w
e
@
us
o
*
@lad
............ ......................@ to0*
....................~~~~~..
..
M ......................
.............. ........................6..y
2 *@*@ @@w*
.... ...
| el @ ...................JR .............6............
*
M,
in......... .........................s
.............. ...............................6
.............. ........................IL.s U.... y
#A ..............
.............. ............................t
*
.
.
@ @@L@ .@ .L
44-i. *90a
. .
. .
.. . .
. .
. .
.
.
.
.
n
.
.
.
.
* **
@
.. . .
*~~~~~~~~~~4 @@@@@***:
* e ee * ** * @ *
*@@ **
*
*@
y
@@
. .
*
. .
.
.
.
. >*@
*z z6
*W
*@ ee :c*o
**
ee
*~~~~~~~~, @@@**@@
.
.
.
.
U
*~~~~~~~~~~I @ @@Cw@@ @@e
*~~~~~~
* | | @ @ e e e @
C,,
*
@
@
@
@
.
. .
*
@
@
@
. .
. .
. .
a.
. .*.
. .
@@@vv@**@
.
.
. .
.
.
.
o * @ e@ @
.
.
.. . ................ .. ....s . . . . @ ** * @ @@ @s @ * * -
@ * * * *-
* .
.
.
@@@@@@ LIJ
.
@'W-
:-NJ
Xyooov,vw,^baoxRooo~aZ oo:g as FwJowy ~~~U;"'V4.14
WooFFay
0.
z4z, ".e
MO,.Woo -.
t"1y7 sgr:F t
691W~~ ~
c~~
Su U.0
--
-oF
|
No. 15 4051
4052 Nucleic Acids Research, Vol. 19, No. 15
Akim
-Cocw-iF.0ta
C%W,6(1*-~ r-
*&-At
.
NiffaiRl nmm
__M I
:T--
RI
;--W-
09vXt 4-a ws s*~~-8 - Xis .
4'S
60.
4@
0
Nucleic Acids Research, Vol. 19, No. 15 4053 CYW%U% WIWI"^
C3,p-s cpN§Fw§w§m9=
W%
m
II-low 0
-
gP.-
-~~~. ata
--
"66 IL
U8.10M.
',-U. )14Sa~~~~~U IL
M-M wurAncx.-O.rl.wlw%
.7..
8:0-,.-Mma ,o,,ol= --Cvc.-O-Ok ,O,.. 000,
-n! -oQair -a- ' Lo-7w&"i"vsyE"zS~Z.c Ixsae tLI i -
I
= aZ . I'l '.
4054 Nucleic Acids Research, Vol. 19, No. 15 WI"
0
0 Ob. 4 CY
.~w
MO~
dL
§i
04-z6
>
b_1
m
ICY _Uowo
4J .u
4.l6
"4 :1''.6
.-J
6
Ks .
S4 0-4
Uzi
IC..
:
01 M4
:
;
:5: *a.
I
I
.4-
4*:
.1
:
- - -- -
-
~~
~~ . 9
~ :4-c
~
~
.F**@w-|@v-sev.yos|@
.*.Fw@ ..v* o7.s=Xu@@--W^tQ_y"M>4FFr">_,w0oi
.c
OMt
.8
-
&
J
I rIltr ajc60 -
:"O:I!l 0
31-
*w*LryL *wZy
4056 Nucleic Acids Research, Vol. 19, No. 15
0Q
o
,-z
2
40
>
*U *
*Z b *o b, *_ *o
, *J
q
00
, *J
g *>e . *S , *_ t *o
5
t x
,*
b *a
b *_
g .>
>,
t
g *z@
2Z w
b *z
*W bg .o
g *.
b*
b *> I *N
t .s *W ' yz
E
E
, .,
b *lu
, *_
.0
, *y
C ~.
_C
orw-
-
, *> , *,
*US
, *y
*X *F
, .,
z
*Ff
, *_
b *W
, *, , *_
I-
*F
< CL Qo_
*
, *,
, *z
,*§
, .o , *, ,* , *y b* > , *> t *U , *, , *,
*E,
b *> , *= , *, ,*
,* , *o
, *v.
, *#
, *,
o .0 _
, *_
b *Q *ffi.
*o l| *J , *_
w ,* *y , .y b *U.
ol
E
*q,:
>
CZ
M
.
0
*y ' yU
64
=V
.L. *F1-
*o
, *s
:Z Z
Q
*_,
*"2
,@
00ce
, *s
, *y ,*,
> *Z , *, *s, ,*, , *,,
o
0
, *o, | *s
*L-,I
, *-
*, *=, *S *s,
*,
.*D
* *CX
*§
*w,
*0
-n
*w
*>
*_
*o, *F *, *Z *Cw *r *w *"
:
:Zs
:y : :0 : *31> *_ ,
I" *lw
*s .
*z *y . *> . *z
*" . *0 |
*y .
40 CD Pt
m E.
I -)R
z o*
>,
88o o "
-I I
@g@
. t.z * . tz-~,a>
.
*tCU
Nucleic Acids Research, Vol. 19, No. 15 4057 0D
0
Oa
0
V It.S-*0
0CuCu0
fC uQ0
~
-SO ou p
pnltobooLo No66'0-0010 N1
0
1--
6.51- U
It
YYV)ntnf
z
L M
0
t>o
0
osto
yy
I
--WWW
0 02..0 §v 4 M~~~~~~~~~~IA.
%U 00.6
* *.15. *-IC VW W W4 * W
USWd :E
Y EOW 3-5.5:
I
J J6
I
U
.6x6
IL
243
4:
IW
W
4> .~~~~~~~~K
4U
*
0 -
W W22
OOZYEda
6--15iw 0-6 '0*
>-3
0
-.U
oLeM0
.0
*
a
C) L0 SWw66DWW .c 0o0o
'9 :
WW
:IL 56
88n
4
0E cm,1
a:
H
W.0tlM
89is°°° U.3
*3 D5 O. 6.
j0W W
a0
»W»W5
: :ffi6a:
c)
Cu
FeentF eg
:Www * *-X * .0
S1.?
zz
* --'*
.-IC
0
000000
*yy *5"-
.UJ..
Ws
C)
W WI *-15 *Y Y *13 1 t MWWW I * 000000@
z
U
3)
22---. YY.
> ..>
C3 06
>~~~~~~~L tu su
He
00-
W zzJ W U0) 0i c
-'. 4
*>>>
4304 * JJ X.*>t>>
63.66it ui Cc O -C
~
0'Z0 .~
0j
U
0:
> > .*
3.
y
U
CD
10
z
.0
*
o
.0
c
:r
* 0 44FF
.
>*
.9.90
*~~~~~~~~~~~~.6 *oam'LJJ . O...'z -.s __ *
N] 61
60
*4 *Ow *
*
y
WWCf!*a *:
|~~-JJ.
@
'* 6-600 0
:
_
*
M> *W>
O 6JW
*
**
::-
.
.
-.
y , y
y
2200 063
nn
.
=
WYtYtY
O
W *
*
IIIAU
.
*3
;*
.J
O
WW
_'_2
4-L
4 '-6-6-6P >>~0. -J >
t
* '*
YJJ
w
* >>> U.
Cu
,*4 WW 6WW>>
0
-ac''0 'ne U4 4 I0 '.6:
-J
U)-C-63. :0 6>> >
-J
J j
"U0.6
v L 6.6.* * * J64y6 J **
uJ w I3
z
0. JjJ *>JJJJ
-z-|. E 43430 43
*)1:22*6
Cu * *YYY
Q8°2°2°°22
U.
.
Cu13X
*
'-3-3ii
oW~~~~~~~CU)Y>* YW °°= 8210t *-*JJ
*
-- el >>
C, * *00WJU"U
CO
*Y=>' CZ
C
Mus---X
* *ov w 00ww ~ *
3*
_____
4IJ3=
*
*
4ooo
:gM yyy Mt Mjgd-eLL As pb
*"*J-J
-i Ww9 *1--08
ogo
seat S
*1 M *oY
.aee,
: : oS=§ Z
HIM0
,XXJ
Y:>
S
0 0
9L J
*:
4
1991
Oxford University Press
Nucleic Acids Research, Vol. 19, No. 15 4045-4057
Compilation and alignment of DNA polymerase
sequences
Junetsu Ito and Dan K.Braithwaite Department of Microbiology and Immunology, College of Medicine, University of Arizona Health Sciences Center, Tucson, AZ 85724, USA Received May 29, 1991; Revised and Accepted July 9, 1991
INTRODUCTION More than 40 different DNA polymerases, including some putative DNA polymerase sequences deduced from nucleotide sequence data, have recently been reported (1-39). The amino acid sequences of these DNA polymerases have been aligned and partial homologous regions identified by many investigators (2-4,9,10,12-25,27-36,42-51). Based on the segmental amino acid sequence similarities, DNA polymerases have been classified into two major groups; E. coli DNA polymerase I-Type and eukaryotic DNA polymerase ca-Type (14,44,47,48,51), or family A DNA polymerases and family B DNA polymerases (4,9,50). As the number of DNA polymerase sequences increases, the classification of DNA polymerases becomes increasingly ambiguous. For example, DNA polymerase delta of yeast was shown to have amino acid sequence similarity to the a-Type DNA polymerases (17). It has become necessary to establish a unified classification of DNA polymerases. Here we propose to classify DNA polymerases into families A, B, and C (Figure 1: A, B, and C), according to the amino acid sequence homologies with E. coli DNA polymerases I, II, and III, respectively. As new and different prokaryotic and eukaryotic DNA polymerases are identified, the number of families can easily be expanded by using additional letters of the alphabet (i.e., D, E, etc.). The bacterium E. coli (strain K12) contains three distinct DNA polymerases I, II, and HI (52). E. coli DNA polymerase I, the first DNA polymerase discovered, is specified by the polA gene (52). E. coli DNA polymerase II, encoded by the polB gene, was recently sequenced and found to be identical to the dinA gene, a DNA damage inducible gene whose expression is regulated by the SOS system in E. coli (8,53). Amino acid sequence alignment shows that E. coli DNA polymerase II has significant homology with family B (a-Type) DNA polymerases (8,53,54). E. coli DNA polymerase IH is a multisubunit enzyme encoded by various dna genes (55); the DNA polymerizing a-subunit encoded by the polC (dnaE) gene (56) and the 3'- 5' exonuclease performing e-subunit encoded by the dnaQ gene (57). The asubunit of E. coli DNA polymerase III exhibits an extensive homology with the corresponding a-subunit of Salmonella typhimurium DNA polymerase m (35); and both show significant homology to Bacillus subtilis DNA polymerase HI, a singlepolypeptide encoded by the polC gene (36). In summary, family A DNA polymerases are named for their homology to the product of the polA gene encoding E. coli DNA polymerase I; family B DNA polymerases are named for their
homology to the product of the polB gene encoding E. coli DNA polymerase 11; and family C DNA polymerases are named for their homology to the product of the polC gene encoding E. coli DNA polymerase HI. The eukaryotic DNA polymerase (3, the smallest known DNA polymerase, does not have homology with those of any of the DNA polymerase families described above. Instead, DNA polymerase (3 has homology with terminal transferases (37). This ,B group we will call family X (Figure ID). The classification and original reference(s) for the amino acid sequences of each DNA polymerase are shown in Table 1. All of the family A DNA polymerases, except for yeast mitochondrial DNA polymerase I, are prokaryotic and are very sensitive to dideoxynucleotide inhibitors, and therefore are useful enzymes for DNA sequencing by the chain-termination method (58). The family A DNA polymerases are resistant to aphidicolin. The family B DNA polymerases are quite extensive in number and variety. Most of the family B DNA polymerases, if not all, are sensitive to aphidicolin and relatively resistant to dideoxynucleotide inhibitors. Most of the family B DNA polymerases, except for pAI2 (33) and yeast DNA polymerase II (16), contain the highly conserved amino acid sequence motif YGDTD, which has been suggested to form part of the dNTP binding site. Amino acid substitutions in this conserved sequence resulted in defects in the DNA polymerase activity without affecting the 3'- 5' exonuclease activity (59,60,61). The family C DNA polymerases are major bacterial replicative DNA polymerases which do not have appreciable homology with those of family A and B DNA polymerases. B. subtilis DNA polymerase Im is a single polypeptide that is highly sensitive to hydroxyphenylazouracil (62). It is anticipated that the number of sequenced family C DNA polymerases will increase rapidly, since all of the aerobic bacteria may contain a member of this family of DNA polymerases.
SEQUENCE ALIGNMENT The 37 complete DNA polymerase sequences and 3 complete terminal deoxynucleotidyltransferase (TDT) sequences are listed in 4 groups; the family A DNA polymerases, the family B DNA polymerases, the family C DNA polymerases, and family X DNA polymerases (including TDTs). In order to limit the space needed for the alignment, we omitted DNA polymerase sequences that are very similar to the prototype DNA polymerase. The DNA polymerases not shown include: herpes virus type-2 (63),
4046 Nucleic Acids Research, Vol. 19, No. 15 adenovius Wpe-S (64), bacteriophage T3 (65), and bacteriophage PZA (66).
ACCURACY OF SEQUENCE DATA Whenever a sequence ambiguity existed in a published sequence, we contacted the authors to obtain the updated sequence a few publisd amino acid sequences information. We found differ at one or more positions from their GenBank/EMBL entry. Again, we have communicated with the primary author to confirm the correct sequences. The multiple alignment of the amino acid sequences was obained by a series of pairwise aligments combined and adjusted by eye into larger and larger subsets of similar sequences. The process of combining and adjusting by eye was aided by modified versions of the MOTIF program (67) and the ALIGN program (68). The GAP and BESTFIT programs, from UWGCG (University of Wisconsin Genetic Computer Group) (69), initay generated the pairwise alignments, adjusted for maximum alignment that allowed for a considerable number of gaps. We then compressed these alignments by eye to give a more contiguous alignment. The alignment of the sequences for optimal similarity is straightforward in the areas of relatively conserved strucure, but is much more arbitary in the more varied sequence areas. The alignment of the varied areas should therefore be regarded as less than optimal in view of the difficulties concerned with multiple alignments in these areas. Finally, we invite fiuther correction from readers, and welcome suggested revisions and altemative alignments.
ACKNOWLEDGEMENTS This work was supported by grant GM28013 from the National Institutes of Health and by grant NP-704 from the American Cancer Society.
REFERENCES 1. Joyce, C.M., Kelley, W.S. and Grindley N.D.F. (1982) J. Biol. Chem. 257, 1958-1964. 2. Lopez, P., Martinez, S., Diaz, A., Espinosa, M. and Lacks, S.A. (1989) J. Bio. Chem. 264, 4255-4263. 3. Lawyer, F.C., Stoffel, S., Saiki, R.K., Myambo, K., Dnmmond, R. and Gelfand, D.H. (1989) J. BRil. Chem. 264, 6427-6437. 4. Leavitt, M.C. and Ito, J. (1989) Proc. NatL. Acad. Sci. U.S.A. 86, 4465-4469.
5. Dunn, J.J. and Stuiier, F.W. (1983) J. Mol. Biol. 166, 477-535.
6. RAdn, B. and Rutberg, L. (1984) J. Virol. 52, 9-15. 7. Foury, F. (1989) J. Biol. Ceem 264, 20552-20560. 8. Iwasaki, H., Ishino, Y., Toh, H., Nakata, A. and Shinagawa, H. (1991)
Mol. Gen. Genet. 226, 24-33. 9. Jung, G., Leavitt, M.C., Hsieh, J.-C. and Ito, J. (1987) Proc. Natt. Acad. Sd. U.S.A. 84, 8287-8291. 10. Savilahti, H. and Bamford D.H. (1987) Gene 57, 121-130. 11. Yoshikawa, H. and Ito, J. (1982) Gene 17, 323-335. 12. Matsumoto, K., Takano, H., Kim, C.I. and Hirokawa, H. (1989) Gene 84, 247-255. 13. Spicer, E.K., Rush, J., Fung, C., Reha-Krantz, L.J., Karam, J.D. and Konigsberg, W.H. (1988) J. Biol Chem. 263, 7478-7486. 14. Wong, S.W., Wahl, A.F., Yuan, P.-M., Arai, N., Pearson, B.E., Arai, K.-i., Korn, D., Hunkapiller, M.W. and Wang, T.S.-F. (1988) EMBO J. 7, 37-47. 15. Pizzagalli, A., Valsasnini, P., Plevani, P. and Lucchini, G. (1988) Proc. Natl. Acad. Sd. U.S.A. 85, 3772-3776. 16. Morison, A., Arad, H., Clark, A.B., Hamatake, R.K. and Sugino, A. (1990) Cell 62, 1143-1151.
17. Boulet, A., Simon, M., Faye, G., Bauer, G.A. and Burgers, P.M.J. (1989) EMBO J. 8, 1849-1854. 18. Morrison, A., Christensen, R.B., Alley, J., Beck, A.K., Bernstine, E.G., Lemontt, J.F. and Lawrence, C.W. (1989) J. Bacteriol. 171, 5659-5667. 19. Gibbs, J.S., Chiou, H.C., Hall, J.D., Mount, D.W., Retondo, M.J., Weller, S.K. and Coen, D.M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 7969-7973. 20. Kouzarides, T., Bankier, A.T., Satchwell, S.C., Weston, K., Tomlinson, P. and Barrell, B.G. (1987) J. Virol. 61, 125-133. 21. Baer, R., Bankier, A.T., Biggin, M.D., Deininger, P.L., Farrell, P.J., Gibson, T.J., Hatfull, G., Hudson, G.S., Satchwell, S.C., S6guin, C., Tuffnell, P.S. and Barrell, B.G. (1984) Nature 310, 207-211. 22. Davison, A.J. and Scott, J.E. (1986) J. Gen. Virol. 67, 1759-1816. 23. Binns, M.M., Stenzler, L., Tomley, F.M., Campbell, J. and Boursnell, M.E.G. (1987) Nucl. Acids Res. 15, 6563-6573. 24. Earl, P.L., Jones, E.V. and Moss, B. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3659-3663. 25. Tomalski, M.D., Wu, J. and Miller, L.K. (1988) Virology 167, 591-600. 26. Gingeras, T.R., Sciaky, D., Gelinas, R.E., Bing-Dong, J., Yen, C.E., Kelly, M.M., Bullock, P.A., Parsons, B.L., O'Neill, K.E. and Roberts, R.J. (1982) J. Biol. Chem. 257, 13475-13491. 27. Engler, J.A., Hoppe, M.S. and van Bree, M.P. (1983) Gene 21, 145-159. 28. Shu, L., Hong, J.S., Wei, Y.-f. and Engler, J.A. (1986) Gene 46, 187-195. 29. Paillard, M., Sederoff, R.R. and Levings, C.S. miI (1985) EMBO J. 4, 1125-1128. 30. Stark, M.J.R., Mileham, A.J., Romanos, M.A. and Boyd, A. (1984) Nucl. Acids Res. 12, 6011-6030. 31. Tommasino, M., Ricci, S. and Galeotti, C.L. (1988) Nucleic Acids Res. 16, 5863-5878. 32. Oeser, B. and Tudzynski, P. (1989) Mot. Gen. Genet. 217, 132-140. 33. Kempken, F., Meinhardt, F. and Esser, K. (1989) Mol. Gen. Genet. 218, 523-530. 34. Tomasiewicz, H.G. and McHenry, C.S. (1987) J. Bacteriol. 169, 5735-5744. 35. Lancy, E.D., Lifsics, M.R., Munson, P. and Maurer, R. (1989) J. Bacteriol. 171, 5581-5586. 36. Hammond, R.A., Barnes, M.H., Mack, S.L., Mitchener, J.A. and Brown, N.C. (1991) Gene 98, 29-36. 37. Mashge, A., Nishikawa, K., Ooi, T., Seto, Y. and Yamaguchi, M. (1987) J. Biol. Chem. 262, 8960-8962. 38. Abbotts, J., SenGupta, D.N., Zmudzka, B., Widen, S.G., Notario, V. and Wilson, S.H. (1988) Biochemistry 27, 901-909. 39. SenGupta, D.N., Zmudzka, B.Z., Kumar, P., Cobianchi, F., Skowronski, J. and Wilson, S.H. (1986) Biochem. Biophys. Res. Com 136, 341-347. 40. Peterson, R.C., Cheung, L.C., Mataliano, R.J., White, S.T., Chang, L.M.S. and Bollum F.J. (1985) J. Biol. Chen. 260, 10495-19502. 41. Koiwai, O., Yokota, T., Kageyama, T., Hirose, T., Yoshida, S. and And, K.-i. (1986) Nulc. Acids Res. 14, 5777-5792. 42. Argos, P., Tucker, A.D. and Phillipson, L. (1986) Virology 149, 208-216. 43. Larder, B.A., Kemp, S.D. and Darby, G. (1987) EMBO J. 6, 160-175. 44. Hall, J.D. (1988) Trends Genet. 4, 42-46. 45. Reha-Krantz, L.J. (1988) J. Mol. Biol. 202, 711-724. 46. Bemad, A., Zaballos, A., Salas, M. and Blanco, L. (1987) EMBO J. 6, 4219-4225. 47. Wang, T.S.-F., Wong, S.W. and Kom, D. (1989) FASEB 3, 14-21. 48. Bernad, A., Blanco, L., Lazaro, J.M., Martin, G. and Salas, M. (1989) Cell 59, 219-228. 49. Polesky, A.H., Steitz, T.A., Grindley, N.D.F. and Joyce, C.M. (1990) J. Biol. Chem. 24, 14579-14591. 50. Ito, J. and Braithwaite, D.K. (1990) Nucl. Acids Res. 18, 6716. 51. Blanco, L., Bernad, A. and Salas, M. (1991) Nucl. Acids Res. 19, 955. 52. Kornberg, A. (1974) DNA replication. W.H. Freeman and Co., San Francisco. 53. Bonner, C.A., Hays, S., McEntee, K. and Goodman M.F. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 7663-7667. 54. Chen, H., Lawrence, C.B., Bryan, S.K. and Moses, R.E. (1990) Nucl. Acids Res. 18, 7185-7186. 55. McHenry, C.S.(1985) Mol. Cell. Biochem 66, 71-85. 56. Shepard, D., Oberfelder, R.W., Welch, M.W. and McHenry, C.S. (1984) J. Bacteriol. 158, 455-459. 57. Scheuerman, R., Tam, S., Burgers, P.M.J., Lu, C. and Echols, H. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 7085-7089. 58. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467. 59. Dorsky, D.I. and Crumpacker, C.S. (1990) J. Virol. 64, 1394-1397. 60. Bemad, A., Lizaro, J.M., Sles, M. and Blano, L. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4610-4614.
Nucleic Acids Research, Vol. 19, No. 15 4047 61. Jung, G., Leavitt, M.C., Schultz, M. and Ito, J. (1990) Biochem. Biophys. Res. Comm. 170, 1294-1300. 62. Neville, M.N. and Brown, N.C. (1972) Nature New Biol. 240, 80-82. 63. Tsurumi, T., Maeno, K. and Nishiyama, Y. (1987) Gene 52, 129-137. 64. Dekker, B.M.M. and Van Ormondt, H. (1984) Gene 27, 115-120. 65. Beck, P.J., Gonzalez, S., Ward, C.L. and Molineux, I.J. (1989) J. Mol. Biol. 210, 687-701. 66. Paces, V., Vlcek, C., Urbanek, P. and Hostomsky, Z. (1985) Gene 38, 45-56. 67. Smith, H.O., Annau, T.M. and Chandrasegaran, S. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 826-830. 68. Doolittle, R.F.and Feng, D.-F. (1990) In Doolittle, R.F. (ed.), Methods in Enzymol. -Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences. Academic Press, New York, Vol. 183, pp. 659-669. 69. Devereux, J., Haeberli, P. and Smithies, 0. (1984) Nucl. Acids Res. 12, 387-395.
Classification of DNA polymerases A.
Family A DNA po e 1.
Bacteral DNA p a) b) c)
2.
References
c ca DNA poiynmrasc I
S&Wwcccus p_m cniae DNA polymerase Themr
I
aquadcu DNA polymerase I
TS DNA polymerase 17 DNA polymerase Spo2 DNA polymerase
(7)
Family B DNA pom 1.
Bacterial DNA pobm E- ci DNA polymerase II
2.
PRDI DNA polymerase5 #29 DNA p merase M2 DNA polymerase T4 DNA p rase
3.
Ekarysodc DNA polymeaes
4.
Human DNA polymerase alpha Yeast DNA polymerase I Yeast DNA polmeras II Yeast DNA poymerase HI (delta) Yeast DNA polymerase Rev3 Viral DNA polymases a) b) c) d) e)
a) b) c) d) e) f)
g) h) i) j) S.
(8)
Bacteriophage DNA polymera
a) b) c) d)
Herpes-1 DNA polymerase Human cytomeplovirus DNA polymerase Epstein-Barr virus DNA polymerase Variceila-Zoster virus DNA polymerase Fowlpox virus DNA polymerase Vaccinia virus DNA polymerase Autographa californica nuclear polyedrosis virus (AcMNPV) DNA polymerase Adenovrus-2 DNA polymerase Adenovirus-7 DNA polymerasel Adenovirus-12 DNA polymerase*
(9,10) (11) (12) (13)
(14)
(15)
(16) (17) (18)
(19) (20) (21) (22) (23) (24) (25) (26)
(27)
(28)
Eukaryotic linear DNA plasmid encoded DNA polymerases a) b) c) d) e)
C
(4) (5) (6)
Mltocho l DNA p merase Yeast mitochondrial DNA polymerase (MIPI)
B.
(1) (2) (3)
Bacteriophage DNA pomerases a) b) c)
3.
ase
S-1 maize mitochondrial DNA polymerase es lacdis plasmid pGKLI DNA polymerase Kyveryces lacts plasmid pGKI2 DNA polymerase Claicep pwpura plasmid pCLKU DNA polymerase Ascobolu unmeu plasmid pAI2 DNA polymerase
Kkqyvw
(29) (30) (31) (32)
(33)
Family C DNA polymerases Bacterial replicative DNA polymerases
a) b) c) D.
E coi DNA polymerase III a subunit Sabnonel yphmwiwu DNA polymerase III a subunit Bacius subi DNA polymerase I
Family X DNA p a) b) c) d) e)
(34) (35)
(36)
a
Rat DNA polymerase ^ Human DNA polymerase 8 Human terminal deaxynucleotidyltransferase (TdT) Bovine terminal deaoynucleotidyltransferase (TdT) Mouse terminal deoxynud1eotiltransferase (dT)
(37) (38,39) (40) (41) (41)
Table 1. The main families and subclassifications of DNA polymerases. Those DNA polymerases marked with a star (*) are protein-primed DNA polymerases.
4048 Nucleic Acids Research, Vol. 19, No. 15 e.Ao
O 0
t%9o
V%0..-40400-.-
0
.N0,1
0o M"D
0o C
CCb.*-GOp
C
018,14rm
0
z
0'Oui0
60
0
v
U
,''''''Yb4. m
99
129-
9-
.199* a
...JbU
1
3
.
Me9~~9
:
0 *.w.. 3b1...b 0u.8..au..
_j
Zli
0
3.. > * * v v v v * @
Ben
w.- .w.
g.
&4-Yb..
J
-a..
, ~~~~~~~~~~~~~~~~~~3 I::
4~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~11 ~ ~ ~ ~ ~ ~ ~ 01. C-Ybb0
b-Yb .L.. so
P.-j.X -o11
.
J
acs
-b
Ez
Of-cafb-Y06
.216a :.J.64:-a.. Jj: 3W -ic wltl*wa
3~~~~!OBS:
:o**v@*0 r2
,
Sb~~~mw
.-11
IZ *
w§
*lu
.J=.
Yb'V'O'
1~2
t
.
@.19..I
.
.
.3
Yb
.
W.*9b
.19. WW
.J 'Ybb
-
J-'.
9.3.Y
J9
W-.5.b 9
_J.J_:j:e
3
.339
@@ :.Z
*@*@
u
*XX
.1W095.3.Yb
..'9bb* b-bLY0b
'
oftf.Yb''''5
V644
~
...Sb.
00az0* 2SI.aea
b-
:IL
-.934 U.5.o . WYbYb 0 ..Yb..3b ..Zs.3 .3...~~~~~~~~~~~~~~~~~9 .J~~~I . b----rd 0~~ :~~~~~~~~~~~~~J395.31
Ii
10
Ybb-0.
.....Yb.
"''"s:
19
~~:::
0 _ Te-3 VW.ISISYb4R:~~~~~~~~~~~a.01
.b made9..9.
~~~Z!8.-*~~~~~~~~~~.
.539.
.
.
Us.
5w53 :::~
~~~~~~~ ..~c- .3 .b .J.. .M :* .w . . v
' . 5YLC.S ::: Yb..0.' 0953 ....4..ie~~~~~~~~~~~~660 YbtY ..b .R -. *9.bYIb6
fMb
r-
PLe..W.J'.99OW.JO.Cq
:
3:
-
00 3
0
. .~..J99 . . Z=QE
*-@
@
co
b
0.~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~5-
~w
I
**-:*:T:
: JYwI..=-.JU. e ::;::: .AC,
$..Wu#
''''' .3
*~ ~ ~ ~ ~ ~''''''3'
q
.3.
:* MUIIA
z
_.9.. ''''''9-e Yb * | * * -< ''*
-JO
3-
P. Yb.C
t
:* a.ss ICIZ
416.J30
3
:W:~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~e
95~~~~~~
...
6
.
z
0..
:-9.
la 0 ~~~::~~~g: :~~~~-~''~~~ 0.-C., ....19..b-~M6 9 Y19950950 3.9-. l..J b--M" M I . Y. -U.5b3 :: ---bI Le 019S1.9b--
03
''-I
0 3W ..9'. bY-zb J-~~~49bYbbb bI 4LYb4.. . ''S'9 Yb bbbbJJ .de0j.....J4 000~~~.b* b- :..O 4--b9.. W,5--J. *
v% >_> im
222J
:.JYb Yb.S'..Qft
4494 Yb44W
.
Ls.
w
.I. mm -da
B
*v "Yb
4L.~~~~~~~~~~~~~~1 .Jb--.
*
*b-02
*
-- i Y4f.Jb5 '"'2.JJJJ-bYb..bb995 AL~~~~~~~~~~~
.Jl9..Ji
.J'''Yb* Wu~~~~~~~~~~~~~~~~3 8L.-.WILM
44b-
YbYb_3
S
9590
AZ _.Jj
.Jb..9J.-
''6b-0Yb.J9Yb b'=.J-
'.W3.0
J 1''.
3U~~:::J: :1 :,-L W -3-
0h9Y. :~: wfat WH
YbCb8b 9 ..o ~ b--bb-3.J4094
:
33_bYb3YY
)
43W0
.J995..-
:
-C
;; 2
'E .1
::*-,IC
UseYb O. 33333
1539
00.YY 'Yb-Yb'a
0
..
0
s300
0b-YYb.a. 000.3
.j..j...js::I:W MCN8 `H :' b-40.0 3.p
-09.JIL
9'OV9N.-
-
#3~~~
3
C-b-Yb00YbYb. 0so M33 LWQ..II,el '0..e OWN
s
AL
_
b.' '06U.
3Y95bJ'**
''3
.
az
tg*
a..a
YbYbb'
W
.di
jcc) oA
_
I
Cz.* silo-
YbY b*-
0
1.11.9-b8.21 ~ b-b-
b-b- 8.2'
9
9-9-82'
V9 -9-82
YbZg ~* YbWm Yz 9~"I
~~ Yb2E~g~* .9
9
Uft~~~~~~~~JL
9
bb-
~
:S19
8C2' t Yb )-,
Nucleic Acids Research, Vol. 19, No. 15 4049 . t-M [email protected] 40
9-~~~~~i ~ ~ CO' : . . .. .090. .N) :
a
51:8 ::s16z .2 B0 :
:
-J..0
I
IC b. R 21I9"'10I 9-. ~
Aj2
0
U1.
23OX ...
0 39-429909 .99U
a W% b
. .~9.9 . ....
*'~~~'9-20~~~~~0. > 0 9~~~~~~~~~~.
.
~~~~~09.J>09 . .. ...
0
9,> >,
.
..
a 5- .5,,g .04MM
0.. 0.09.5. 09... W.
'IliI I0I00.
9096 "9-.>
5i. 5
9-9 .
u 0=90 Sa .a5099.6 ..-j
.
-
:IU6
_
6~9
.OL
c
:dLdLfx
_
9-
U09
209099.9-il.
929RJ
20-' 092094
.
9:L
09~~~~~~~~__j09 6_J .L.jjW
IUAW -ldC
9404a
O.-
..oi9 .0908ou.0 L E N.9
.N.j
W9 UWO%9 au
9-
:I-j~~~ a
J
40 409-
9
00
.09..J~~~09. 0 . .= to2
.. .09..i
. ..
.092092..~E.003 ::
.p.09.
..mI;-.M.. .s ~~~~~~-.~~~~~~~~~09 .
.h *2 0109 99-3
:8~~~~ul2ge3:: a
"I0
:
:
:§ 09
u -
in N
I
e
'-V
4
I
C&~9.
"& U'99
"1*9I~
II»ow>-.t&.,&a!)0 4
~~~~~~~:.6..1
9
USa u9.
4050 Nucleic Acids Research, Vol. 19, No. 15 ,;v O--o-NtOM
Go
C44cu-plgDa -C%IA;"=-4r-.0,00P.40"lnM= 4or-*;::9:8s ---
.
zuw_o=n
_s
zzw .
.
V33~~~~~ .o~ ." i.y .> . . .F< .
se***,. .. .. . . .iC
..2 .
.
IM
-MU-.*
** ~~ ~ ~J@ ~ * ~ *__~~~~ xa
~~~
.
.
. ..
*
.
*
.
O
*
t*
bd
@
sc
~ @@ed** J **** U.
*_ *@** *_U* M6o*
.~~~~~C . = tAV*rr_x
**.Z. ffi=:|72,ip * * *sOsy@iEg . . . .a
IW
ya.... :=>la *B*YYYyw~t * @ t >0..@-
* @** J_J
* @@ttW_z
. . v^ w
@
>||D-* --
_>
L
z
*qF
*
*-
-^la @
_
_
*@ @@""
W
* .....
cp-OYFo
---A-MUMS
9--
0
7= A>0 . rL ,.L- =3= z,9W,-6-0.0.4irIfi.-VI-i -
-
>-
c
-
--
9s
I
: .0 H :
,
U;
41 -1
. @ * s@
.. . . . . Fy
Nucleic Acids Research, Vol. 19,
0---*-O,-,Ol ;iz:!a O-t-w,oln
---o-o--=aN S'..
O-. 0
Ca 0NIN-0O 00
M OOCM
rowr owrl NNEJuu -
1............
cl ........... .....................|| w*3 * @ e e e e
o
w
e
@
us
o
*
@lad
............ ......................@ to0*
....................~~~~~..
..
M ......................
.............. ........................6..y
2 *@*@ @@w*
.... ...
| el @ ...................JR .............6............
*
M,
in......... .........................s
.............. ...............................6
.............. ........................IL.s U.... y
#A ..............
.............. ............................t
*
.
.
@ @@L@ .@ .L
44-i. *90a
. .
. .
.. . .
. .
. .
.
.
.
.
n
.
.
.
.
* **
@
.. . .
*~~~~~~~~~~4 @@@@@***:
* e ee * ** * @ *
*@@ **
*
*@
y
@@
. .
*
. .
.
.
.
. >*@
*z z6
*W
*@ ee :c*o
**
ee
*~~~~~~~~, @@@**@@
.
.
.
.
U
*~~~~~~~~~~I @ @@Cw@@ @@e
*~~~~~~
* | | @ @ e e e @
C,,
*
@
@
@
@
.
. .
*
@
@
@
. .
. .
. .
a.
. .*.
. .
@@@vv@**@
.
.
. .
.
.
.
o * @ e@ @
.
.
.. . ................ .. ....s . . . . @ ** * @ @@ @s @ * * -
@ * * * *-
* .
.
.
@@@@@@ LIJ
.
@'W-
:-NJ
Xyooov,vw,^baoxRooo~aZ oo:g as FwJowy ~~~U;"'V4.14
WooFFay
0.
z4z, ".e
MO,.Woo -.
t"1y7 sgr:F t
691W~~ ~
c~~
Su U.0
--
-oF
|
No. 15 4051
4052 Nucleic Acids Research, Vol. 19, No. 15
Akim
-Cocw-iF.0ta
C%W,6(1*-~ r-
*&-At
.
NiffaiRl nmm
__M I
:T--
RI
;--W-
09vXt 4-a ws s*~~-8 - Xis .
4'S
60.
4@
0
Nucleic Acids Research, Vol. 19, No. 15 4053 CYW%U% WIWI"^
C3,p-s cpN§Fw§w§m9=
W%
m
II-low 0
-
gP.-
-~~~. ata
--
"66 IL
U8.10M.
',-U. )14Sa~~~~~U IL
M-M wurAncx.-O.rl.wlw%
.7..
8:0-,.-Mma ,o,,ol= --Cvc.-O-Ok ,O,.. 000,
-n! -oQair -a- ' Lo-7w&"i"vsyE"zS~Z.c Ixsae tLI i -
I
= aZ . I'l '.
4054 Nucleic Acids Research, Vol. 19, No. 15 WI"
0
0 Ob. 4 CY
.~w
MO~
dL
§i
04-z6
>
b_1
m
ICY _Uowo
4J .u
4.l6
"4 :1''.6
.-J
6
Ks .
S4 0-4
Uzi
IC..
:
01 M4
:
;
:5: *a.
I
I
.4-
4*:
.1
:
- - -- -
-
~~
~~ . 9
~ :4-c
~
~
.F**@w-|@v-sev.yos|@
.*.Fw@ ..v* o7.s=Xu@@--W^tQ_y"M>4FFr">_,w0oi
.c
OMt
.8
-
&
J
I rIltr ajc60 -
:"O:I!l 0
31-
*w*LryL *wZy
4056 Nucleic Acids Research, Vol. 19, No. 15
0Q
o
,-z
2
40
>
*U *
*Z b *o b, *_ *o
, *J
q
00
, *J
g *>e . *S , *_ t *o
5
t x
,*
b *a
b *_
g .>
>,
t
g *z@
2Z w
b *z
*W bg .o
g *.
b*
b *> I *N
t .s *W ' yz
E
E
, .,
b *lu
, *_
.0
, *y
C ~.
_C
orw-
-
, *> , *,
*US
, *y
*X *F
, .,
z
*Ff
, *_
b *W
, *, , *_
I-
*F
< CL Qo_
*
, *,
, *z
,*§
, .o , *, ,* , *y b* > , *> t *U , *, , *,
*E,
b *> , *= , *, ,*
,* , *o
, *v.
, *#
, *,
o .0 _
, *_
b *Q *ffi.
*o l| *J , *_
w ,* *y , .y b *U.
ol
E
*q,:
>
CZ
M
.
0
*y ' yU
64
=V
.L. *F1-
*o
, *s
:Z Z
Q
*_,
*"2
,@
00ce
, *s
, *y ,*,
> *Z , *, *s, ,*, , *,,
o
0
, *o, | *s
*L-,I
, *-
*, *=, *S *s,
*,
.*D
* *CX
*§
*w,
*0
-n
*w
*>
*_
*o, *F *, *Z *Cw *r *w *"
:
:Zs
:y : :0 : *31> *_ ,
I" *lw
*s .
*z *y . *> . *z
*" . *0 |
*y .
40 CD Pt
m E.
I -)R
z o*
>,
88o o "
-I I
@g@
. t.z * . tz-~,a>
.
*tCU
Nucleic Acids Research, Vol. 19, No. 15 4057 0D
0
Oa
0
V It.S-*0
0CuCu0
fC uQ0
~
-SO ou p
pnltobooLo No66'0-0010 N1
0
1--
6.51- U
It
YYV)ntnf
z
L M
0
t>o
0
osto
yy
I
--WWW
0 02..0 §v 4 M~~~~~~~~~~IA.
%U 00.6
* *.15. *-IC VW W W4 * W
USWd :E
Y EOW 3-5.5:
I
J J6
I
U
.6x6
IL
243
4:
IW
W
4> .~~~~~~~~K
4U
*
0 -
W W22
OOZYEda
6--15iw 0-6 '0*
>-3
0
-.U
oLeM0
.0
*
a
C) L0 SWw66DWW .c 0o0o
'9 :
WW
:IL 56
88n
4
0E cm,1
a:
H
W.0tlM
89is°°° U.3
*3 D5 O. 6.
j0W W
a0
»W»W5
: :ffi6a:
c)
Cu
FeentF eg
:Www * *-X * .0
S1.?
zz
* --'*
.-IC
0
000000
*yy *5"-
.UJ..
Ws
C)
W WI *-15 *Y Y *13 1 t MWWW I * 000000@
z
U
3)
22---. YY.
> ..>
C3 06
>~~~~~~~L tu su
He
00-
W zzJ W U0) 0i c
-'. 4
*>>>
4304 * JJ X.*>t>>
63.66it ui Cc O -C
~
0'Z0 .~
0j
U
0:
> > .*
3.
y
U
CD
10
z
.0
*
o
.0
c
:r
* 0 44FF
.
>*
.9.90
*~~~~~~~~~~~~.6 *oam'LJJ . O...'z -.s __ *
N] 61
60
*4 *Ow *
*
y
WWCf!*a *:
|~~-JJ.
@
'* 6-600 0
:
_
*
M> *W>
O 6JW
*
**
::-
.
.
-.
y , y
y
2200 063
nn
.
=
WYtYtY
O
W *
*
IIIAU
.
*3
;*
.J
O
WW
_'_2
4-L
4 '-6-6-6P >>~0. -J >
t
* '*
YJJ
w
* >>> U.
Cu
,*4 WW 6WW>>
0
-ac''0 'ne U4 4 I0 '.6:
-J
U)-C-63. :0 6>> >
-J
J j
"U0.6
v L 6.6.* * * J64y6 J **
uJ w I3
z
0. JjJ *>JJJJ
-z-|. E 43430 43
*)1:22*6
Cu * *YYY
Q8°2°2°°22
U.
.
Cu13X
*
'-3-3ii
oW~~~~~~~CU)Y>* YW °°= 8210t *-*JJ
*
-- el >>
C, * *00WJU"U
CO
*Y=>' CZ
C
Mus---X
* *ov w 00ww ~ *
3*
_____
4IJ3=
*
*
4ooo
:gM yyy Mt Mjgd-eLL As pb
*"*J-J
-i Ww9 *1--08
ogo
seat S
*1 M *oY
.aee,
: : oS=§ Z
HIM0
,XXJ
Y:>
S
0 0
9L J
*:
4
