For all species, the process of DNA replication requires the use of multiple different DNA polymerase enzymes. The primary function of these unique multisubunit enzymes is to ensure optimal DNA stability for an accurate replication process.
Functions of DNA polymerase enzymes
Since Arthur Kornberg was awarded the Nobel Prize in 1959 for determining the roles of DNA polymerases during DNA replication, it has been widely accepted that the DNA polymerases involved in this process require a single-stranded template to construct a new DNA strand.
In addition to DNA polymerase, DNA replication also requires several other enzymes including a helicase to unwind the double-stranded template DNA, as well as a primase to assemble a short RNA primer.
The DNA polymerase enzymes involved in the eukaryotic DNA replication belong to the B family of DNA polymerases, whereas those enzymes that function in bacteria belong to families A and C, and those of archaea belong to families B and D.
It has been determined that all replicative DNA polymerases contain additional domains that function to facilitate interactions with other proteins, 3’ to 5’ exonucleolytic proofreading and several other important biological processes. During replication, DNA polymerases are involved in copying both DNA strands from the template strand at each replication fork.
Types of DNA polymerase enzymes
Replisomes are large multiprotein assemblies that contain DNA polymerases, helicases, primases, sliding clamps and other important structures involved in DNA replication. Within the highly complicate replisome structure of eukaryotic cells, three different B-family DNA polymerases exist, of which include the multisubunit polymerases Pol α, Pol δ and Pol ε. In addition to carrying out DNA synthesis, B-family DNA polymerases are also responsible for DNA repair and recombination metabolic processes
The functions of Pol α, which is comprised of four different subunits, is to synthesize a considerable amount of DNA, as well as associate with DNA primase to give the Pol α–DNA primase complex. This complex is comprised of four subunits that include the POLA, which is the catalytic subunit, POLA2, which is the regulatory subunit, and the two primase subunits PRIM1 and PRIM2.
The Pol α–DNA primase complex creates RNA-DNA primers. Note that Pol α does not exhibit any proofreading activity; therefore, any errors made by this enzyme will be corrected by other mechanisms, of which include those performed by Pol ε and Pol δ.
The synthesis of DNA on both the leading and lagging strands is accomplished by both Pol ε and Pol δ. Both Pol ε and Pol δ are highly accurate and processive enzymes that utilize their exonuclease activities for proofreading processes during replication. Pol δ, which is a three subunit enzyme, is encoded by the POLD1 gene, whereas Pol ε, a four subunit enzyme, is encoded by the POLE gene.
Non-replicative/specialized DNA polymerase enzymes
While replicative DNA polymerases only function during cell division, non-replicative or specialized DNA polymerases are used throughout the lifecycle of the cell. The emergence of specialized DNA polymerases has provided insight into how these enzymes play a role in preventing replicative stress and its devastating consequences during DNA replication.
These monomeric enzymes primarily belong to the Y family, of which include Pol η, ι, κ and Rev1 polymerases; however, additional enzymes of the B-family, such as Pol, and the X family, such as Pol θ, fall into this category of specialized DNA polymerases.
Pol of the B-family plays a role in the embryonic development of mammals, whereas Pol θ of the X family has been described for its role in lesion bypass, base excision repair mechanisms and somatic hypermutation.
The DNA polymerases of the Y family exhibit a wide variety of cellular functions, many of which are involved in maintaining different types of stability within the cell. For example, Pol η and κ play a role in maintaining the stability of fragile sites (FS) in mammalian cells, which are considered to be the most sensitive components of the genome. In fact, the sensitivity of common fragile sites (CFS) on chromosomes to experience stress after replication has been linked with causing cancer-specific chromosomal rearrangements.
The X family of nonreplicative polymerases, which can be found in all species, particularly vertebrates that carry all four types of these polymerases, include Pols β, λ and μ, as well as the homolog deoxyribonucleotidyltransferase (TdT).
The X family polymerases contain highly conserved regions that include two helix-hairpin-helix domains that are essential to their interaction with DNA. One of these motifs is found in a domain that interacts with downstream DNA and the other is found in the thumb domain which works together with the primer strand to help begin the process of DNA replication.
Pol β, which is encoded by the POLB gene in humans, has been shown to participate in different DNA repair and damage tolerance pathways. More specifically, Pol β performs short patch repair of damaged DNA by fixing alkylated, oxidized or abasic sites that have formed as a result of DNA damage. Although this polymerase does not exhibit any proofreading activity on its own, its precise selectivity for correct nucleotides that reduces the chance of errors to occur when in use.
Pol λ and Pol μ, which are encoded by the POLL and POLM genes, respectively, are involved in the rejoining of breaks that have occurred in double strands of DNA that occur following exposure to hydrogen peroxide, as in the case of Pol λ, or ionizing radiation, as in the case of Pol μ, which is an enzyme that is predominantly found in lymphoid tissue.
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