101
Pol α (primase) consists of four subunits, two α and two-subunit primase which
are encoded by the POLA1 and POLA2 genes. The primary role of this enzyme is
the initiation of the leading strand DNA replication and in the repeated priming of
Okazaki fragments during lagging-strand DNA replication. The DNA pol α holoenzyme possesses two distinct yet functionally interacting active sites: one in the
large subunit responsible for the DNA synthesis, and one in the dimeric primase
responsible for the RNA synthesis [15]. Once primase has created the RNA primer,
pol α starts replication elongating the primer with ~ 20 nucleotides.
Due to their high processivity, pol ε and pol δ take over from pol α the leading
and lagging strand synthesis, respectively [16]. Pol δ is expressed by genes polD1,
creating the catalytic subunit, polD2, polD3, and polD4 creating the other subunits
that interact with the Proliferating Cell Nuclear Antigen (PCNA) which is a DNA
clamp that allows pol δ to possess processivity [3, 16]. Pol ε is encoded by the polE,
the catalytic subunit, polE2, and polE3 genes. While pol ε’s main function is to
extend the leading strand during replication, pol ε’s C-terminus region is thought
to be essential to cell vitality as well. The C-terminus region is thought to provide
a checkpoint before entering anaphase, to provide stability to the holoenzyme, and
to add proteins to the holoenzyme, necessary for the initiation of replication [3, 17].
Pol ζ, another B family polymerase, is made of two subunits Rev3, the catalytic
subunit, and Rev7, which increases the catalytic function of the polymerase, and
is involved in the translesion synthesis [18]. Pol ζ lacks 3′–5′ exonuclease activity,
and is unique in that it can extend primers with terminal mismatches. Rev1 has
three regions of interest in the BRCT domain, ubiquitin-binding domain, and Cterminal domain, and has dCMP transferase ability, which adds deoxycytidine opposite lesions that would stall replicative polymerases pol δ and pol ε. These stalled
polymerases activate ubiquitin complexes, which in turn disassociate replication
polymerases and recruit pol ζ and Rev1. Together, pol ζ and Rev1 add deoxycytidine and pol ζ extends past the lesion. Through a yet undetermined process, pol ζ
disassociates and replication polymerases reassociate and continue replication. pol
ζ and Rev1 are not required for replication, but loss of REV3 gene in budding yeast
can cause increased sensitivity to DNA-damaging agents due to collapse of replication forks where replication polymerases have stalled [18].
4.2.2.3 Family C
Family C of DNA polymerases is presented exceptionally by bacterial enzymes
involved in replicative processes. So, the DNA polymerase III holoenzyme is the
main enzyme realizing the DNA replication in Escherichia coli, Bacillus subtilis,
and belongs to family C polymerases. It consists of three assemblies: the pol III
core, the beta sliding clamp processivity factor and the clamp-loading complex. The
core consists of three subunits—α, the polymerase activity hub, ε, exonucleolytic
proofreader, and θ, which may act as a stabilizer for ε. The holoenzyme contains
two cores, one for each strand, the lagging and leading [19]. The beta sliding clamp
processivity factor is also present in duplicate, one for each core, to create a clamp
4 DNA Dependent DNA Polymerases as Targets for Low-Weight …
Pol α (primase) consists of four subunits, two α and two-subunit primase which
are encoded by the POLA1 and POLA2 genes. The primary role of this enzyme is
the initiation of the leading strand DNA replication and in the repeated priming of
Okazaki fragments during lagging-strand DNA replication. The DNA pol α holoenzyme possesses two distinct yet functionally interacting active sites: one in the
large subunit responsible for the DNA synthesis, and one in the dimeric primase
responsible for the RNA synthesis [15]. Once primase has created the RNA primer,
pol α starts replication elongating the primer with ~ 20 nucleotides.
Due to their high processivity, pol ε and pol δ take over from pol α the leading
and lagging strand synthesis, respectively [16]. Pol δ is expressed by genes polD1,
creating the catalytic subunit, polD2, polD3, and polD4 creating the other subunits
that interact with the Proliferating Cell Nuclear Antigen (PCNA) which is a DNA
clamp that allows pol δ to possess processivity [3, 16]. Pol ε is encoded by the polE,
the catalytic subunit, polE2, and polE3 genes. While pol ε’s main function is to
extend the leading strand during replication, pol ε’s C-terminus region is thought
to be essential to cell vitality as well. The C-terminus region is thought to provide
a checkpoint before entering anaphase, to provide stability to the holoenzyme, and
to add proteins to the holoenzyme, necessary for the initiation of replication [3, 17].
Pol ζ, another B family polymerase, is made of two subunits Rev3, the catalytic
subunit, and Rev7, which increases the catalytic function of the polymerase, and
is involved in the translesion synthesis [18]. Pol ζ lacks 3′–5′ exonuclease activity,
and is unique in that it can extend primers with terminal mismatches. Rev1 has
three regions of interest in the BRCT domain, ubiquitin-binding domain, and Cterminal domain, and has dCMP transferase ability, which adds deoxycytidine opposite lesions that would stall replicative polymerases pol δ and pol ε. These stalled
polymerases activate ubiquitin complexes, which in turn disassociate replication
polymerases and recruit pol ζ and Rev1. Together, pol ζ and Rev1 add deoxycytidine and pol ζ extends past the lesion. Through a yet undetermined process, pol ζ
disassociates and replication polymerases reassociate and continue replication. pol
ζ and Rev1 are not required for replication, but loss of REV3 gene in budding yeast
can cause increased sensitivity to DNA-damaging agents due to collapse of replication forks where replication polymerases have stalled [18].
4.2.2.3 Family C
Family C of DNA polymerases is presented exceptionally by bacterial enzymes
involved in replicative processes. So, the DNA polymerase III holoenzyme is the
main enzyme realizing the DNA replication in Escherichia coli, Bacillus subtilis,
and belongs to family C polymerases. It consists of three assemblies: the pol III
core, the beta sliding clamp processivity factor and the clamp-loading complex. The
core consists of three subunits—α, the polymerase activity hub, ε, exonucleolytic
proofreader, and θ, which may act as a stabilizer for ε. The holoenzyme contains
two cores, one for each strand, the lagging and leading [19]. The beta sliding clamp
processivity factor is also present in duplicate, one for each core, to create a clamp
4 DNA Dependent DNA Polymerases as Targets for Low-Weight …