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J Bacteriol, April 1998, p. 2232-2236, Vol. 180, No. 8
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
A Novel DNA Polymerase Family Found in
Archaea
Yoshizumi
Ishino,1,*
Kayoko
Komori,1
Isaac K. O.
Cann,1 and
Yosuke
Koga2
Department of Molecular Biology, Biomolecular
Engineering Research Institute, Suita, Osaka
565-0874,1 and
Department of Chemistry,
University of Occupational and Environmental Health, Kitakyushyu
807-0804,2 Japan
Received 6 November 1997/Accepted 22 January 1998
 |
ABSTRACT |
One of the most puzzling results from the complete genome sequence
of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is
because no other DNA polymerase-like open reading frames (ORFs) were
found besides one ORF having the typical 
-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the
second DNA polymerase) from the hyperthermophilic archaeon Pyrococcus furiosus, which has also at least one -like
DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino,
Genes Cells 2:499-512, 1997). The genes in M. jannaschii
encoding the proteins that are homologous to the DNA polymerase II of
P. furiosus have been located and cloned. The gene products
of M. jannaschii expressed in Escherichia coli
had both DNA polymerizing and 3'
5' exonuclease activities. We
propose here a novel DNA polymerase family which is entirely different
from other hitherto-described DNA polymerases.
| |
TEXT |
DNA polymerases play leading
roles in cellular DNA replication and repair. They can be classified
into four major groups based on amino acid sequences (8).
Family A includes the most abundant DNA polymerases in eubacterial
cells, such as Escherichia coli DNA polymerase I (Pol I).
All of the replicative DNA polymerases from eucaryotic and eubacterial
cells belong to families B and C, respectively. Family X consists of
eucaryotic DNA polymerase 
and terminal transferases.
The domain Archaea is now recognized as constituting a third
major branch of life, together with Bacteria (eubacteria)
and Eucarya (eucaryotes) (17). Archaeal proteins
involved in gene expression, such as those for DNA replication,
transcription, and translation, have been found to be similar to those
from Eucarya, although the cellular appearance and
organization of Archaea are more like those of
Bacteria. All of the sequences of the archaeal DNA
polymerases thus far are classified as -like (family B) DNA polymerases. Among them, two hyperthermophilic archaea,
Pyrodictium occultum and Sulfolobus solfataricus,
possess two (14) and three (5) -like DNA
polymerase genes, respectively, although it has not been proved
whether two of the three genes in S. solfataricus are
expressed to produce active DNA polymerases. This finding tempted us to
speculate that the DNA replication machinery in Archaea may
be a prototype of the eucaryotic machinery, because three -like DNA
polymerases (, 
, and 
) function in eucaryotic DNA replication
(reviewed in reference 1).
The first complete sequence of an archaeal genome, from
Methanococcus jannaschii, which is a methane-producing
archaeon, was published in 1996 (2). Surprisingly, it was
found that this genome includes only one open reading frame with a
sequence homologous to -like DNA polymerases and lacks other DNA
polymerase sequences. One of the most controversial issues from the
first complete genome sequence from Archaea is whether this
organism indeed possesses only one DNA polymerase (3, 4, 6,
11). More definitely, it would be very surprising if the life of
this archaeon were dominated by only a single DNA polymerase with a
unique mechanism, since it is well established that both eucaryotic and
eubacterial cells contain several DNA polymerases involved in
replication and repair.
Search for homologs of Pyrococcus furiosus DP1
and DP2.
Recently, we found novel DNA polymerase genes in the
hyperthermophilic archaeon P. furiosus, which encode a
product that is completely distinct from any other known DNA polymerase
(16). This DNA polymerase is composed of two different
polypeptides, DP1 (69 kDa) and DP2 (143 kDa). We have searched the
complete genome sequence of M. jannaschii and have found two
open reading frames, MJ0702 and MJ1630, with sequences that are highly
homologous to the two subunits of P. furiosus, i.e., DP1
(40%) and DP2 (60%), respectively (Fig.
1). We cloned the two genes from the
total DNA of M. jannaschii by PCR and constructed an
expression system with the pET21a plasmid (Novagen). The resultant
plasmids were designated pMJDP1 and pMJDP2, respectively.
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FIG. 1.
Alignment of the two components of DNA Pol II from
P. furiosus and M. jannaschii. (A and B) DP2 and
DP1, respectively. CLUSTAL W (13) was used for sequence
alignment of the two polymerases. Identical and similar amino acid
residues at the same positions are indicated by asterisks and dots,
respectively, in both alignments.
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|
Identification of DNA polymerase and 3'5' exonuclease
activity.
Sonicated cell extracts from E. coli
BL21(DE3), carrying either plasmid pMJDP1 or pMJDP2, were heat treated
at 80°C for 15 min to inactivate the DNA polymerase activities from
the host E. coli cells. Then, the DNA polymerase activity at
65°C was measured with these extracts (heated extract [HE]). The
reaction mixtures contained, in 40 µl, 20 mM Tris-HCl (pH 8.8), 2 mM
MgCl2, 2 mM -mercaptoethanol, 0.2 mg of calf thymus
activated DNA per ml, 40 µM deoxynucleoside triphosphate (dNTP)
containing 60 nM [methyl-3H]TTP, and protein
samples and were incubated at 65°C for 10 min. The results
demonstrated that the radioactivity was incorporated into
acid-insoluble fraction only by the mixture of two extracts from
BL21(DE3)/pMJDP1 (HE1) and BL21(DE3)/pMJDP2 (HE2). Neither extract exhibited the incorporation activity individually (Fig. 2A). To prove its DNA polymerizing
activity more definitively, a chain elongation assay was done with a
single-stranded DNA (prepared from plasmid p240C, which has an
insert of 40 bp, dCGATAAGGGCAACGAATCCATGTGGAGAAGAGCCTCTATA, at the HincII site of pUC118) annealed with a
32P-labeled d40-mer with the above sequence as a template
primer in a reaction mixture containing 20 mM Tris HCl (pH 8.8), 2 mM MgCl2, 2 mM -mercaptoethanol, and 83 µM dNTPs. As
shown in Fig. 2B, the 32P-labeled primer was extended by
the combined extract (HE1-HE2), even though the degradation of the
primer was faster. The 3'5' exonuclease activity was also
investigated. The 32P-labeled d40-mer was used as a
substrate directly (for single-stranded substrate) or after being
annealed with p240CS single-stranded DNA (for double-stranded
substrate) and was incubated with the proteins in the reaction mixture
described above without dNTPs. The 3'5' exonuclease activity was
also detected only when the two extracts were mixed (Fig.
3). Therefore, we conclude that the
mixture of the two gene products (69 and 129 kDa) is essential for the
emergence of the DNA polymerase and 3'5' exonuclease activities,
just as in the case of P. furiosus. These two genes were
designated polB and polC, respectively, and the
gene products were designated M. jannaschii Pol II (M. jannaschii has a gene encoding a protein with the sequence of
typical -like DNA polymerases as described above) according to the
corresponding genes and their products in P. furiosus
(16).
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FIG. 2.
Detection of the DNA polymerizing activity from
the MJ0702 and MJ1630 proteins. The reaction conditions are described
in the text. (A) The acid-insoluble radioactivity bound to DE 81 paper
detected by a scintillation counter. Protein samples are indicated
under the bar graph as follows: EHE, HE from BL21(DE3)/pET21a;
DP1, HE from BL21(DE3)/pMJDP1; DP2, HE from BL21(DE3)/pMJDP2. Lanes 1 and 5, H2O; lane 2, 14 µg; lanes 3 and 4, 7.0 µg
each; lane 6, 1.75 µg each; lane 7, 3.5 µg each; lane 8, 5.25 µg
each; lane 9, 7.0 µg each; lanes 10 to 14, DP1 (7.0 µg) and various
amounts of DP2 (lane 10, 0 µg; lane 11, 1.75 µg; lane 12, 3.5 µg; lane 13, 5.25 µg; and lane 14, 7.0 µg). (B) Chain
elongation ability detected by a primer extension reaction with a
single-stranded DNA annealed with a 32P-labeled d40-mer
(described in the text) as a template primer. Equal amounts were
sampled at 2, 5, 10, and 15 min from the reaction mixture and
loaded onto an 8% polyacrylamide gel containing 8 M urea. The
electrophoretic profile was visualized by autoradiography.
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FIG. 3.
Detection of the 3'5' exonuclease activity from the
MJ0702 and MJ1630 proteins. For the 3'5' exonuclease assay, equal
aliquots of the reaction mixture described in the text were removed
after 2, 5, 10, and 15 min and were added to a stop solution. Products
were analyzed by polyacrylamide gel electrophoresis in the presence of
8 M urea as described for Fig. 2B. ds, double stranded; ss, single
stranded.
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|
Inhibition analysis of the DNA polymerase activity.
The
inhibition mode of the DNA polymerizing activity of M. jannaschii Pol II was investigated by using representative
inhibitors of DNA polymerases. Aphidicolin did not inhibit the activity
of M. jannaschii Pol II with the concentration that
inhibited P. furiosus Pol I, an -like DNA polymerase
(15). Instead, M. jannaschii Pol II was more
sensitive to ddTTP, N-ethylmaleimide, and salt than was P. furiosus Pol I (Fig. 4). These
characteristics are the same as those of P. furiosus Pol II
(7), and this pattern is different from that of other known
DNA polymerases (10).
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FIG. 4.
Inhibition of the DNA polymerizing activity of M. jannaschii Pol II (DP1-DP2) by aphidicolin, ddTTP,
N-ethylmaleimide (NEM), and salt. The standard assay mixture
containing [methyl-3H]TTP for DNA polymerizing
activity as described in the text was processed in the presence of the
indicated amounts of inhibitors. Acid-insoluble radioactivities were
counted with a scintillation counter. The open squares and circles
indicate M. jannaschii Pol II and P. furiosus Pol
I, respectively.
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|
A new DNA polymerase family in Archaea.
We have
also detected genes within Pyrococcus woesei that encode
proteins homologous to DP1 and DP2 (unpublished data). Therefore, we
now propose a new DNA polymerase family, which is characterized by
archaeal heterodimeric DNA polymerases. The functional properties, such
as a concomitant strong 3'5' exonuclease activity and an excellent
primer extension ability (16), suggest that the DNA polymerases belonging to this family may play a crucial role in DNA
replication. In comparison with the excellent primer elongation ability
in vitro of P. furiosus Pol II in our previous report with
the purified proteins (16), the ability of M. jannaschii Pol II (HEs from recombinant E. coli
strains) in this study was very poor. The possibility that some
inhibitor is included in the HE or that M. jannaschii Pol II
may need some auxiliary proteins for its maximal processivity has to be
addressed. This new DNA polymerase found in the two archaea shows no
sequence homology to those of any other families. Therefore, it is
possible that the catalytic center of this DNA polymerase comprises two
separate gene products, which differs from the previous findings that
all DNA polymerases contain their own definite catalytic centers in single polypeptides. We can also envisage a situation where the auxiliary component activates a novel type of catalytic subunit by a
conformational change, removal of a repressor, or some other mode. As
we continue to investigate this DNA polymerase, the mechanism will be
unravelled.
The gene organization of the components of the new polymerase is
also very interesting. The two responsible genes are arranged
in tandem
and constitute an operon in both
P. furiosus and
P. woesei. In contrast, the two genes are completely separated in
the
genome of
M. jannaschii (Fig.
5). It is advantageous to coordinate
the
expression of the two genes for adjustment of the amount of
the two
components of Pol II in the cells, and therefore, it is
intriguing to
imagine how the gene expression of Pol II is regulated
in
M. jannaschii.
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FIG. 5.
Localization of the two genes corresponding to the
new DNA polymerase in the genomes of P. furiosus and
M. jannaschii. The locations of the genes in M. jannaschii follow the published map. The location of the P. furiosus operon is indeterminate, due to the absence of a complete
genomic sequence.
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|
At the moment, most studies of DNA replication are concentrated
on the initiation stage in both
Bacteria and
Eucarya. Although
these studies have provided many important
insights into the roles
of the proteins in the DNA replication process,
there are still
many problems to be elucidated with respect to the
complicated
molecular mechanisms of DNA replication, such as how the
various
DNA polymerases share their roles in DNA synthesis. A BLAST
search
for homologs in the current databases did not reveal any protein
or open reading frame with significant similarity to either MJ0702
or
MJ1630; however, some proteins related to DNA replication with
local
similarities were listed as described in the study of
P. furiosus (
16). Two more complete genome sequences from
the archaeal
domain were published very recently, and we have found the
homologs
of DP1 and DP2 in the genomes of these organisms,
Archaeoglobus fulgidus (
9) and
Methanobacterium thermoautotrophicum (
12).
We now
have the opportunity to analyze the sequences of the four
archaeal
proteins in detail and may be able to predict some motifs
including
critical residues for polymerizing and nucleolytic activities
from
the comparison with other known polymerases. Our finding
of this novel
DNA polymerase family in
Archaea should contribute
to a
better understanding of the functional and evolutionary aspects
of the
replication machineries in the three branches of life.
| |
ACKNOWLEDGMENTS |
We thank Kosuke Morikawa for critical reading of the manuscript.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565, Japan. Phone: 81-6-872-8203. Fax:
81-6-872-8219. E-mail: ishino{at}beri.co.jp.
| |
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J Bacteriol, April 1998, p. 2232-2236, Vol. 180, No. 8
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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