DNA polymerases, 60 years of discoveries - Roger Woodgate Lab

Timeline of DNA discoveries.


The first enzyme capable of copying DNA was discovered in E.coli extracts and was assumed at that time to be the only bacterial DNA polymerase [1]. Later, when a second E. coli DNA polymerase was purified, this enzyme playing an important role in prokaryotic DNA replication and repair was named pol I. The polA gene was sequenced in 1982 [2] (accession P00582a).


The first eukaryotic DNA polymerase was identified [3]. When the uniform nomenclature was adopted in 1975, this enzyme was appropriately designated as pol α. Originally assumed to bear the sole responsibility for DNA synthesis in mammalian cells, this polymerase instead plays a key role in the initiation of chromosomal replication. The POLA gene was sequenced in 1988 [4] (accession CAA29920).


An enzyme with DNA polymerase activity was isolated from the rat liver mitochondria [5, 6]. This enzyme, known since 1977 as pol g [7] is a major polymerase dealing with all transactions involving mitochondrial DNA in mammalian cells. The POLG gene was sequenced in 1995 [8] (accession CAA88012).


A second DNA polymerase was discovered in E.coli by several groups in the USA and Germany [9-11]. According to the chronological order of discovery, it was named pol II. The sequencing of the polB gene was accomplished in 1990 [12] (accession P21189).


During the course of purification of E.coli pol II, a third prokaryotic DNA polymerase was detected [13]. DNA polymerase III is now known to be the main prokaryotic replicative polymerase. The dnaE gene encoding the catalytic a-subunit of pol III was sequenced in 1987 [14] (accession P10443).

A second eukaryotic nuclear DNA polymerase later named pol β, was identified in mammalian cells and tissues practically simultaneously by several laboratories in the USA and England [15-19]. Very soon, it became apparent that this polymerase does not play a direct role in DNA replication. Instead, extensive research conducted by various groups revealed a major role for DNA pol β in base-excision repair. The POLB gene was sequenced in 1986 [20] (accession P06766).


Aformal nomenclature designating each mammalian DNA polymerase with a Greek symbol was proposed in 1974 and accepted by attendees of the international conference on eukaryotic DNA polymerases in 1975 [21].According to the establishednomenclature, the first two mammalian DNA polymerases were designated pols α and β. It is worth noting that the third DNA polymerase which was given the name pol γ was and a forth DNA polymerase found in mitochondria  (designated DNA polymerase-mt) were later shown to be identical and the name pol γ has been retained for this mitochondrial polymerase [7].


The first nuclear polymerase containing an associated 3'®5' exonuclease activity was purified and called pol δ [22]. Later, this polymerase was shown to be an essential component of the eukaryotic replication machinery. The sequencing of the POLD1 gene was accomplished in 1989 [23] (accession P15436).


It was proposed that DNA polymerases should be classified into discrete families based on their evolutionary relatedness. The first two evolutionary groups of DNA polymerases were designated as polymerase families A- and B- according to the amino acid homology to E coli pols I and II, respectively [24]. In 1991 two additional groups typified by the catalytic subunit of E coli pols III and eukaryotic pol β were designated as families C- and X-, respectively [25]. In 1999 family D- was proposed to group polymerases involved in the DNA replication machinery of the Euryarchaeota [26]. In 2001, proteins originally defined as belonging to the UmuC/DinB/Rev1/Rad30 superfamily and involved in mutagenesis and TLS DNA synthesis were designated as Y-family polymerases [27].


The fourth nuclear DNA polymerase in mammalian cells, pol ε, was first reported as a PCNA-independent form of pol δ [28]. Subsequently, this enzyme was recognized as a distinct DNA polymerase and accordingly it was named pol ε. Similar to pol δ, pol ε is equipped with 3'®5' exonuclease proofreading activity and is essential for replication of the eukaryotic genome. The POLE1 gene was sequenced in 1990 [29] (accession P21951).


Saccharomyces cerevisiae DNA pol ζ was characterized as a complex of Rev3 and Rev7 proteins [30]. These studies confirmed the hypothesis that the Rev3 gene long known to be involved in damage-induced and spontaneous mutagenesis, encodes the first DNA polymerase specializing in TLS [31] (accession P14284). This prediction was made based on the homology of Rev3 to other genes encoding B-family DNA polymerases.

In the same year, the same group discovered dCMP transferase activity for the S. cerevisiae REV1 protein [32] that was know at the time to be required for the damage-induced mutagenesis and having ~25% identity with the E.coli UmuC protein [33] (accession P12689). It was proposed that the CMP transferase function was important for mutagenic TLS involving pol ζ. However, Rev1 was not recognized as belonging to the broad superfamily of DNA-dependent DNA polymerases until 1999, when deoxynucleotidyl transferase activity was detected in several enzymes homologous to REV1.


The first evidence suggesting that the E. coli UmuD'2C complex consisting of the umuDC gene products [34] [35] (accession P04152), s a DNA polymerase was demonstrated [36]. At that time, it was shown that in vitro the UmuD'2C complex could copy an abasic site-containing DNA template without the assistance of any other polymerase, although the possibility of contamination with trace amounts of other DNA polymerase were not entirely ruled out. A year later, additional biochemical studies unequivocally confirmed that the UmuD'2C complex is a bona fide DNA polymerase designated as E.coli pol V [37].


The S.cerevisiae RAD30 gene which was previously identified by sequence homology to prokaryotic UmuC and DinB in 1996 [38, 39] was shown to encode DNA polymerase η [40]. Shortly thereafter, human polymerase η was characterized [41]. Polη became one of the founding members of the new Y-family of DNA polymerases [27]. Nonsense, or frameshift mutations in the gene (RAD30A, POLH, XPV) encoding pol ηare responsible for the Xeroderm Pigmentosum Variant syndrome in humans [41, 42].

The same week that the DNA polymerase activity of the UmuD'2C encoded pol V was confirmed, a manuscript describing the TLS activity of E.coli DinB was published [43]. This polymerase became known as E.coli DNA pol IV. The dinB gene was originally identified as dinP in 1995 [44] (accession BAA07593) and despite being shown to be allelic with dinB in 1999 the name of dinP, rather than the correct name of dinB, is still often used in Genbank data files describing related proteins.


The TLS activity of two eukaryotic Y-family polymerases ι [45] and κ [46] (products of POLI (RAD30B) and POLK (DINB1) genes, respectively) was demonstrated a year after they were cloned [47, 48] [accession numbers AAD50381 (pol ι) and AAF02541 pol κ)].

Three X-family polymerases implicated in participating in different types of DNA transactions (such as BER, non-homologous end joining repair, V(D)J recombination, TLS, and sister chromatid cohesion) were discovered. This includes pol λ [49] (the sequence was first submitted in 1998 [50] [accession number CAB65241]), pol μ [51] (accession CAB65075), and pol σ [52] (first sequenced in 1995 [53] accession P53632). It should be noted that the DNA polymerase activity of pol σ has been contested by Haracska et al., [54], who suggest that the protein is actually a poly-A RNA polymerase, rather than a bona fide DNA polymerase.


Two mammalian A-family DNA polymerases that are homologous to the DNA cross-link sensitivity protein Mus308 and implicated in different defense pathways against DNA damage were identified and characterized; pol q [55] and pol ν [56]. It worth mentioning that pol q, the only polymerase known to contain a helicase domain, was first identified in 1997 in the genomes of a variety of eukaryotic organisms based on sequence homology to E. coli DNA pol I [57-59] (accession numbers AAB67306 and AAC33565). The polymerase was originally named pol η [60], but was later renamed pol q [61]. Pol ν was sequenced in 2003 [56] (accession NP_861524).


An ability to replicate both damaged and undamaged DNA templates was detected in PrimPol, an enzyme belonging to the archaeal-eukaryotic primase superfamily [62, 63]. The gene encoding PrimPol was first sequenced in 2005 [64] (accession NP_689896). The ability to catalyze TLS is only one of the broad enzymatic activities of the PrimPol enzymes that have been implicated in a large variety of cellular functions.

a GeneBank Sequence identifiers are listed [65].


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