JOURNAL OF VIROLOGY, Aug. 2000, p. 7079–7084 Vol. 74, No.

15
0022-538X/00/$04.00⫹0
Copyright © 2000, American Society for Microbiology. All Rights Reserved.

A Hypothesis for DNA Viruses as the Origin of Eukaryotic

Replication Proteins
LUIS P. VILLARREAL1* AND VICTOR R. DEFILIPPIS2
Departments of Molecular Biology and Biochemistry1 and Ecology and Evolutionary Biology,2
University of California, Irvine, California 92697

Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP

Received 16 December 1999/Accepted 1 May 2000

The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and
bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus
replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from
phycodnavirus (which infects microalgae) as the basis of this analysis, as it represents a virus of a primitive
eukaryote. We show that it has significant similarity with replicative DNA polymerases of eukaryotes and
certain of their large DNA viruses. Sequence alignment confirms this similarity and establishes the presence
of highly conserved domains in the polymerase amino terminus. Subsequent reconstruction of a phylogenetic
tree indicates that these algal viral DNA polymerases are near the root of the clade containing all eukaryotic
DNA polymerase delta members but that this clade does not contain the polymerases of other DNA viruses. We
consider arguments for the polarity of this relationship and present the hypothesis that the replication genes
of DNA viruses gave rise to those of eukaryotes and not the reverse direction.

Divergence of the bacterial and eukaryotic lineages appears
to represent the deepest split in the tree of life (22). Because
the DNA replication proteins of these groups are of funda-
mental importance and interact through complex mechanisms,
it seems likely that the genome replication system, like the
translational system, would contain the most conserved co-
evolved genes among all related lineages.
Obvious functional homologues of replication genes are
found in bacteria, eukaryotes, and archaea, including proteins
involved in origin recognition, helicases, DNA-binding pro-
teins, DNA synthesis, sliding clamp processivity factors
(PCNA), ligation, and primer removal (see reference 7 and
references therein). However, there are clear differences in
sequence similarity that separate the replication proteins of
bacteria from those of the archea and eukaryotes (7). The
bacterial replication genes thus appear evolutionarily unre-
lated to those of eukaryotes and archaea. For example, the
replicative DNA polymerase (Pol) III of Escherichia coli be-
longs to the family C DNA Pol group and does not have
similarity to either of the two mammalian replicative DNA
family B DNA Pols (alpha priming and delta extending; see
reference 30). As such, phylogenetic analysis of these replica-
tive DNA Pols results in polyphyletic groupings that are con-
trary to accepted species trees (6). Such wide existence of
functionally identical yet nonorthologous genes presents a di-
lemma when they are being used for connecting the universal
tree of life, and this has led some to propose that the cenan-
cestor of bacteria, archea, and eukaryotes had an RNA ge-
nome (7, 17). However, it is now clear that between bacteria
and eukaryotes, perhaps several hundred functional genes are
homologous (e.g., DNA synthesis genes). This suggests that
the putative prokaryotic-eukaryotic ancestor possessed many
genes inherited by both lineages (for references, see references
14 and 8). Proper replicative transmission of such a large
number of essential genes seems unlikely given the small size
* Corresponding author. Mailing address: Department of Molecular
Biology and Biochemistry, 3205 Bio Sci II, University of California,
Irvine, Irvine, CA 92697. Phone: (949) 824-6074. Fax: (949) 824-8551.
E-mail: lpvillar@uci.edu.
of RNA genomes and the error-prone nature of their replica-
tion (14). It therefore appears more likely that the common
ancestor had a DNA genome, which leaves unexplained how
the replication systems underwent the transition during the
divergence of bacteria from archaea and eukaryotes.
DNA viruses, however, also possess a full set of independent
DNA replication and repair proteins that include members of
family A and B DNA Pols (12). When first sequenced, it was
noteworthy how similar phage T4 DNA Pol was to DNA Pols
alpha and delta of eukaryotes, Epstein-Barr virus, human cy-
tomegalovirus, and other DNA viruses of eukaryotes, but not
adenoviruses or E. coli Pol I or III (23). This similarity includes
the conservation of five of six sequential domains (31), as well
as resistance to various family B-specific inhibitors (3). Other
phage DNA Pols, however, such as T7, show similarity to
bacterial DNA Pol I but not to Pols of eukaryotes. With the
sequencing of the entire T4 genome, it was additionally sur-
prising to see that this strictly lytic bacteriophage had more
genes similar to those of eukaryotes (including genes for self-
splicing RNA [13]) than to bacterial genes (4). Viruses are
usually thought to impose negative selection on their hosts. In
addition, recombination between host and viral genomes is a
commonly observed phenomenon, such as with retroviruses
acquiring cellular protooncogenes (5, 28). Yet viruses are
rarely considered a source of host genes, and hence viral se-
quences are not taken into account when reconstructing the
tree of life. However, a viral genome can evolve up to a million
time faster than that of its host. If a DNA virus could impose
a stable persistent (or genomic) infection on its host, it might
then also provide genes altering host evolution, as we have
previously reasoned (29). This raises the question: Could a
DNA virus have been the origin of replicative eukaryotic DNA
Pols?
In this report, we consider the hypothesis for the viral origin
of eukaryotic replication proteins in the context of DNA vi-
ruses that infect host species which are likely representative of
the earliest eukaryotes. We examine DNA Pols from two fam-
ilies of DNA viruses prevalent as acute infections of parasitic
microalgae (Chlorella-like viruses) (27) and persistent infec-
tions of filamentous brown algae (Feldmania species virus) (9,

7079
Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP

7080
VOL. 74, 2000 VIRAL ORIGIN OF EUKARYOTIC REPLICATION PROTEINS
15, 16, 21, 27). These algal species represent some of the
earliest eukaryotes for which clear archaeological data exist
(11). We perform sequence similarity and phylogenetic analy-
ses which indicate that these viral proteins appear related to
the progenitor of all eukaryotic Pol delta sequences and con-
sider arguments that a DNA virus may have been the origin of
the eukaryotic DNA replication system.
MATERIALS AND METHODS
The open reading frame that codes for the DNA Pol or Pol-like gene from
Chlorella virus (NT2A; GenBank M86836; 913 amino acids [a.a.]) and Feldmania
species virus (GenBank AF013260; 996 a.a.) were retrieved from GenBank.
Using these sequences, a gapped Tblastn (version 2.0.4) analysis against the
translated nonredundant database was performed. It was observed that essen-
tially all of the replicative DNA family B Pols from eukaryotes showed similarity
to both sequence probes. In addition, the DNA Pol sequences from most large
DNA viruses of animals were also identified. Although the analysis suggests that
all eukaryotic replicative DNA Pols (alpha and delta) are similar, the DNA Pol
delta genes were most similar to these phycodnavirus-like genes. Interestingly,
although Feldmania virus and Chlorella virus are both DNA viruses of algae, each
of these DNA Pol sequences was more similar to a lower eukaryotic host DNA
Pol gene (Schizosaccharomyces pombe, Candida albicans, Glycine max, or Sac-
charomyces cerevisiae) than to each other. In addition, the DNA Pols of several
lytic phages (T4 and RB69) were identified. Also present were the DNA Pol II
genes from various archaebacterial and bacterial (i.e., nonreplicative E. coli)
species. Absent were the replicative DNA polymerases (Pol III) and Pol I from
bacteria as well as the DNA Pols of other lytic phages (T7), adenoviruses, and
related linear plasmids of fungi.
Following the elimination of redundant and incomplete proteins, the remain-
ing sequences were aligned using ClustalW to aid in identification of homologous
regions. After this alignment, four regions (labeled I, II, III, and IV) of high
conservation were easily identifiable between most of the taxa and are shown
listed in color patterns corresponding to similar amino acids and in biologically
related groups (Fig. 1). As had previously been established, the family B poly-
merase sequences contain up to six specific domains (23, 31). We compared our
conserved domains to those previously identified and determined that our re-
gions II, III, and IV corresponded roughly to the respective regions II, III, and
IV which were identified in DNA Pol alpha by Wang et al. and that our region
I had been previously identified as the phosphonoacetic acid-resistant domain of
herpes simplex virus type 1 DNA Pol in the study to T4 DNA Pol by Spicer et al.
(23). Because there is large variation in length among these DNA Pol genes, the
sequences are shown as a roughly proportional line drawing in which the loca-
tions of the four highly conserved domains are indicated, and the sequences were
centered to the most highly conserved region II domain (Fig. 2). The two
smallest sequences correspond to fragments of Micromonas pusilla virus and
Chrysochromulina species virus (phycodnavirus). The next largest was the full
gene (313 a.a.) for the Pol alpha of Endotrypanum (Leishmania) monterogeni,
then the Helicoverpa armigera nuclear polyhedrosis virus DNA Pol (623 a.a.), and
all other genes were complete sequences. The largest gene (encoding 1,855 a.a.)
was the DNA Pol alpha of Plasmodium falciparum. In general, domains I and II
are adjacent to each other and occur at variable positions from the amino
terminus, although some Archaea species Pol II genes have a region I domain
well displaced toward the amino terminus. With the exception of Halteria species
DNA Pol alpha (ciliated hypotrichous), the order of the domains was conserved,
although DNA Pol alpha genes of hyptrochous species were often lacking do-
mains II and IV. In addition, the DNA Pol II of several archaea (lineage A) had
domains III and IV displaced well towards the carboxy terminus.
These highly conserved regions were then used to aid in the alignment of the
remaining regions as follows. First, using the sequence editor GeneDoc version
2.5 (18), each taxon was examined to determine which if any of the four domains
were present in the protein sequence. Next, these regions were used as anchors
from which to optimize the alignment of amino acids in the intervening sections.
These interregion sequences were extracted and aligned using ClustalW. Fol-
lowing this procedure, the alignments were again optimized by eye, focusing
mostly on the similarity within each of the major clades. Once an overall align-
ment was obtained, a phylogenetic tree was constructed using the more con-
served amino terminus of the protein sequence that included region I and amino
acids thereafter. Phylogenetic analysis was performed using the neighbor-joining
algorithm with 500 bootstrap replications (20) as implemented by PAUP version
4.0b2 (25). Pairwise distances were calculated as mean observed substitutions per
site. The unrooted tree is shown in Fig. 3 and is color coded to mark clear clades.
FIG. 1. Amino acid alignment of four highly conserved DNA Pol protein regions. Taxon names are color coded according to clade as in Fig. 3 and are labeled A0
to L5 according to the branch tips therein. Gaps inserted to improve the alignment are indicated by a dash (—). Amino acids are color coded according to side group
properties using the following scheme: red, negatively charged (D or E); orange, positively charged (H, K, or R); light green, amide (N or Q); blue, alcohol (S or T);
purple, aliphatic (L, I, or V); gray, aromatic (F, Y, or W); brown, small (A or G); dark green, sulfur-containing (M or C); white, proline (P). Abbreviations: Hu, human;
VZV, varicella-zoster virus; HSV, herpes simplex virus; cytomeg., cytomegalovirus; HHV, human herpesvirus.
7081
RESULTS
The results suggest that the relationships are robust: 68% of
the nodes had ⬎90% bootstrap frequency support, and all
nodes were ⬎50%. The unrooted tree shows DNA Pol se-
quences falling into seven clades that correspond to biologi-
cally coherent gene sets. The two largest clades correspond to
variants of DNA Pol alpha (pink) and DNA Pol delta, respec-
tively. In the DNA Pol delta clade (black), the Feldmania
species virus (which causes a prevalent persistent infection of
Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP
filamentous brown algae) DNA Pol is near the base (labeled
pol delta) and the Chlorella-like viral Pol genes are slightly
more derived. Other Pol delta proteins appear to correspond
roughly with accepted evolutionary relationships. The topology
of the DNA Pol alpha group is more complex. Near its root,
the trypanosomes and Leishmania species branch first, fol-
lowed by insects and mammals, which, interestingly, are
grouped separately from Saccharomyces and Schizosaccharo-
myces pombe. Also branching near the base of this clade are
the macronuclear genes of various binucleated hypotrich spe-
cies.
There are three distinct clades of viral DNA Pols. Two of
these correspond to the poxvirus family (light gray) and the
baculoviruses of insects that includes the nucleopolyhedrosis
virus family (green). Both of these groups branch from the
most unresolved region at the center of the tree. The third
clade corresponds to the animal herpesviruses (red). It is in-
teresting that the herpesviruses appear to share an ancestor
with the Feldmania DNA Pol, which corresponds to the base of
the cellular DNA Pol delta clade. The herpesviruses are fur-
ther branched into three monophyletic subgroups correspond-
ing to the alphaherpes-, gammaherpes-, and cytomegalovi-
ruses. The placement of the herpesvirus ancestor near the
unresolved center of the tree suggests a very old origin of these
genes.
The remaining two groups include the replicative DNA Pol
II genes from various archaea (methanogens and Thermococ-
cus, Pyrococcus, and Sulfolobus species), which were known to
be similar to family B DNA Pols (19). DNA Pol II of archaea
species appears to exist as two distinct lineages, both of which
are thought to be involved in genome replication (7, 26). The
larger of these groups appear to share an ancestor with the
DNA Pol alpha genes (blue). The smaller clade (gold) corre-
sponds to DNA Pols found in Solfolobus and pyrodiococci
archaea species. The archaeal DNA Pols on this smaller
branch are closer but not directly connected to the Pol delta
group. This cluster is rooted near the unresolved center of the
tree. Also originating near the unresolved center are the Pols
from lytic phages T4 and RB69 and from E. coli DNA Pol II
(nonessential Pol).
DISCUSSION
With sequences obtained from a similarity search using
DNA Pols from DNA viruses that infect microalgae and fila-
mentous brown algae as a probe, we generated a phylogeny in
which the base of the monophyletic group containing the rep-
licative DNA Pol delta of eukaryotes resembles viral se-
quences. Although an earlier analysis of DNA Pol genes gave
7082 VILLARREAL AND DEFILIPPIS
FIG. 2. Protein map indicating proportional lengths of DNA Pol (black lines) and relative locations of the four conserved Pol protein domains (labeled I to IV).
Proteins are mostly “centered” so that region II is aligned.
rise to similar patterns, the authors did not attempt to explain
this result (6). Since it is unrooted, the phylogeny does not
directly establish the polarity or direction of evolutionary
change. It therefore remains formally possible that the phy-
codnaviruses acquired DNA Pol genes from their algal hosts
and maintained similarity to them for unknown reasons. As the
algal host DNA Pol genes have not been sequenced, we cannot
place them on this tree. Even if they were subsequently to be
placed phylogenetically near the phycodnavirus genes, this
would still be unlikely to resolve the issue of evolutionary
direction. However, we believe several considerations argue
that the direction of transmission was from virus to host. First,
only under this circumstance could the dilemma of dissimilar
replication genes now present in bacteria and eukaryotes be
resolved. In addition, all the other viral DNA Pols examined
form distinct monophyletic groups (i.e., herpesviruses, poxvi-
ruses, and baculoviruses) that do not include host Pols. There-
fore, these other viruses did not appear to acquire their Pol
genes from a host species. The DNA delta clade is clearly
monophyletic yet includes all the diverse phycodnavirus Pols of
both microalgal and filamentous algal hosts. Thus, the phycod-
J. VIROL.
Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP
naviruses are clearly evolutionarily exceptional DNA viruses.
The simplest way to account for these observations is to pro-
pose that host Pol delta genes are derived from an early DNA
viral gene that resembles that present in Feldmania virus.
Trees of life have been generated using different genes,
yielding multiple evolutionary histories (8). Phylogenetic anal-
ysis of DNA Pol sequences presents patterns inconsistent with
accepted organismal phylogenies. These phylogenetic dispari-
ties are difficult to explain if most genetic variation during
evolution of species occurs by random genetic change and
vertical gene transmission. Genomic analysis has suggested
that horizontal transfer of gene sets may have been more
prevalent then previously believed, especially in bacterial spe-
cies. Horizontal transmission of DNA replication genes, how-
ever, would suggest the transfer of fundamental, complex, cel-
lular components and the involvement of a DNA virus. We
have argued that the persistence of a genetic parasite (a virus
or its defective derivatives) is a life strategy that can allow the
superimposition of complex molecular genetic control systems
onto its host (29). As such, a persistent agent (like Feldmania
virus) can potentially provide new systems of genetic control,
VOL. 74, 2000
FIG. 3. Unrooted neighbor-joining phylogeny based on amino-terminal portion of DNA Pol protein sequences as discussed in the text. Labels at branch tips
represent taxa as presented in Fig. 1. Numbers at branch nodes indicate percent bootstrap support for that node based on 500 replications.
including genome replication, to its host, particularly if it is
integrated into the genome. We suggest at least in the case of
DNA Pol delta an evolutionary link of the bacteria and eu-
karyota (and archaea) via the DNA Pol of an ancient DNA
virus, not the replicative host genes. Our analysis also suggests
that DNA Pol alpha may share an ancestor with DNA Pol II of
archaea that diverged after the initial divergence of bacteria
from eukaryotes and archaea. Two other DNA Pols resemble
the family B replicative Pols of eukaryotes and archaea. One is
the nonessential Pol II of E. coli, and the other is the Pol from
lytic phages T4 and RB69. Both branch from the largely un-
resolved center of the tree. As the phages represent a much
more transmissible system than E. coli Pol II, and as T-like
phages infect both bacteria and archaea (Euryachaeota king-
dom [32]), it is easier to envision substitution of functional
homologues for DNA replication genes if such a virus was
involved. Other DNA replication genes may also fit this pat-
tern, since it is known that DNA viruses also code for various
ligases, helicases, and PCNA-like genes as well as “repair-like”
DNA Pols, such as DNA Pol beta, found in entomopoxvirus
(1).
Many of the crucial regulatory genes of DNA viruses, such
as the T antigens of polyomaviruses, have no known host an-
alogues, even though these viruses are phylogenetically con-
VIRAL ORIGIN OF EUKARYOTIC REPLICATION PROTEINS 7083
Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP
gruent with their host species over long periods of time (29).
Thus, at least for these regulatory genes, they are viral, not
host, creations. Viral genomes can evolve much faster than
host genomes, and populations are known to exhibit much
greater genetic variability, as demonstrated by the frequent
occurrence of mutants and defectives. Thus, viral systems have
an enhanced capacity to produce genetic novelty. Although
some examples of virus-mediated horizontal gene transfer
have recently been proposed (2), in most of these proposals it
is suggested that the host, not the virus, is the original source
of the transferred gene. We now suggest that such infectious
and/or persisting agents may be a general source for acquisi-
tion of complex molecular systems and phenotypes.
ACKNOWLEDGMENT
This research was supported by the Irvine Research Unit in Animal
Virology.
REFERENCES
1. Afonso, C. L., E. R. Tulman, Z. Lu, E. Oma, G. F. Kutish, and D. L. Rock.
1999. The genome of Melanoplus sanguinipes entomopoxvirus. J. Virol. 73:
533–552.
2. Baldo, A. M., and M. A. McClure. 1999. Evolution and horizontal transfer of
dUTPase-encoding genes in viruses and their hosts. J. Virol. 73:7710–7721.
3. Bernad, A., A. Zaballos, M. Salas, and L. Blanco. 1987. Structural and
7084 VILLARREAL AND DEFILIPPIS
functional relationships between prokaryotic and eukaryotic DNA poly-
merases. EMBO J. 6:4219–4225.
4. Bernstein, H., and C. Bernstein. 1989. Bacteriophage T4 genetic homologies
with bacteria and eucaryotes. J. Bacteriol. 171:2265–2270.
5. Bishop, J. M. 1983. Cellular oncogenes and retroviruses. Annu. Rev. Bio-
chem. 52:301–354.
6. Braithwaite, D. K., and J. Ito. 1993. Compilation, alignment, and phyloge-
netic relationships of DNA polymerases. Nucleic Acids Res. 21:787–802.
7. Edgell, D. R., H. P. Klenk, and W. F. Doolittle. 1997. Gene duplications in
evolution of archaeal family B DNA polymerases. J. Bacteriol. 179:2632–2640.
8. Forterre, P. 1999. Displacement of cellular proteins by functional analogues
from plasmids or viruses could explain puzzling phylogenies of many DNA
informational proteins. Mol. Microbiol. 33:457–465.
9. Goldbach, R., and P. De Haan. 1994. RNA viral supergroups and the evo-
lution of RNA viruses, p. 105–119. In S. S. Morse (ed.), The evolutionary
biology of viruses. Raven Press, Ltd., New York, N.Y.
10. Kapp, M. 1998. Viruses infecting marine brown algae. Virus Genes 16:111–
117.
11. Knoll, A. H. 1992. The early evolution of eukaryotes: a geological perspec-
tive. Science 256:622–627.
12. Knopf, C. W. 1998. Evolution of viral DNA-dependent DNA polymerases.
Virus Genes 16:47–58.
13. Kutter, E., K. Gachechiladze, A. Poglazov, E. Marusich, M. Shneider, P.
Aronsson, A. Napuli, D. Porter, and V. Mesyanzhinov. 1995. Evolution of
T4-related phages. Virus Genes 11:285–297.
14. Lake, J. A., R. Jain, and M. C. Rivera. 1999. Mix and match in the tree of life.
Science 283:2027–2028.
15. Mueller, D. G., M. Braeutigam, and R. Knippers. 1996. Virus infection and
persistence of foreign DNA in the marine brown alga Feldmannia simplex
(Ectocarpales, Phaeophyceae). Phycologia 35:61–63.
16. Muller, D. G., M. Sengco, S. Wolf, M. Brautigam, C. E. Schmid, M. Kapp,
and R. Knippers. 1996. Comparison of two DNA viruses infecting the ma-
rine brown algae Ectocarpus siliculosus and E. fasciculatus. J. Gen. Virol.
77:2329–2333.
17. Mushegian, A. R., and E. V. Koonin. 1996. A minimal gene set for cellular
life derived by comparison of complete bacterial genomes. Proc. Natl. Acad.
Sci. USA 93:10268–10273.
18. Nicholas, K. B., H. B. Nicholas Jr., and D. W. Deerfield II. 1997. GeneDoc:
analysis and visualization of genetic variation. EMBNEW.NEWS 4:14.
(http://www.cris.com/⬃ketchup/genedoc.shtml) annotating multiple se-
quence alignments, version 2.5.
J. VIROL.
19. Pisani, F. M., C. De Martino, and M. Rossi. 1992. A DNA polymerase from
the archaeon Sulfolobus solfataricus shows sequence similarity to family B
DNA polymerases. Nucleic Acids Res. 20:2711–2716.
20. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method
for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.
21. Sengco, M. R., M. Braeutigam, M. Kapp, and D. G. Mueller. 1996. Detection
of virus DNA in Ectocarpus siliculosus and E. fasciculatus (Phaeophyceae)
from various geographic areas. Eur. J. Phycol. 31:73–78.
22. Sogin, M. L., J. H. Gunderson, H. J. Elwood, R. A. Alonso, and D. A. Peattie.
1989. Phylogenetic meaning of the kingdom concept: an unusual ribosomal
RNA from Giardia lamblia. Science 243:75–77.
23. Spicer, E. K., J. Rush, C. Fung, L. J. Reha-Krantz, J. D. Karam, and W. H.
Downloaded from http://jvi.asm.org/ on July 18, 2018 by UNIVERSIDAD AUTONOMA DE SLP
Konigsberg. 1988. Primary structure of T4 DNA polymerase. Evolutionary
relatedness to eucaryotic and other procaryotic DNA polymerases. J. Biol.
Chem. 263:7478–7486.
24. Staskawicz, B. J., F. M. Ausubel, B. J. Baker, J. G. Ellis, and J. D. Jones.
1995. Molecular genetics of plant disease resistance. Science 268:661–667.
25. Swofford, D. L. 1993. PAUP: a computer program for phylogenetic inference
using maximum parsimony. J. Gen. Physiol. 102:9A.
26. Uemori, T., Y. Ishino, H. Doi, and I. Kato. 1995. The hyperthermophilic
archaeon Pyrodictium occultum has two alpha-like DNA polymerases. J.
Bacteriol. 177:2164–2177.
27. Van Etten, J. L. 1994. Algal viruses, p. 35–40. In R. G. Webster and A.
Granoff (ed.), Encyclopedia of virology, vol. 1. Academic Press, Inc., San
Diego, Calif.
28. Varmus, H. E. 1984. The molecular genetics of cellular oncogenes. Annu.
Rev. Genet. 18:553–612.
29. Villarreal, L. P. 1999. DNA virus contribution to host evolution, p. 391–420.
In E. Domingo, R. G. Webster, and J. J. Holland (ed.), Origin and evolution
of viruses. Academic Press, San Diego, Calif.
30. Wang, C. C., L. S. Yeh, and J. D. Karam. 1995. Modular organization of T4
DNA polymerase: evidence from phylogenetics. J. Biol. Chem. 270:26558–
26564.
31. Wang, T. S., S. W. Wong, and D. Korn. 1989. Human DNA polymerase
alpha: predicted functional domains and relationships with viral DNA poly-
merases. FASEB J. 3:14–21.
32. Zillig, W., D. Prangishvilli, C. Schleper, M. Elferink, I. Holz, S. Albers, D.
Janekovic, and D. Gotz. 1996. Viruses, plasmids and other genetic elements
of thermophilic and hyperthermophilic Archaea. FEMS Microbiol. Rev.
18:225–236.