Translesion DNA polymerases in eukaryotes: what makes them tick? - PubMed (original) (raw)

Figure 1. DNA polymerases: 60 years of discoveries

1956 – 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 (Kornberg et al., 1956). Later, when a second E. coli DNA polymerase was purified, this enzyme which plays an important role in prokaryotic DNA replication and repair was named pol I. The polA gene was sequenced in 1982 (Joyce et al., 1982) (accession P00582a). 1957 – The first eukaryotic DNA polymerase was identified (Bollum and Potter, 1957). 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 (Wong et al., 1988) (accession CAA29920). 1968 – An enzyme with DNA polymerase activity was isolated from the rat liver mitochondria (Kalf and Ch’ih, 1968; Meyer and Simpson, 1968). This enzyme, known since 1977 as pol γ (Bolden et al., 1977) is a major polymerase dealing with all transactions involving mitochondrial DNA in mammalian cells. The POLG gene was sequenced in 1995 (Ropp and Copeland, 1995) (accession CAA88012). 1970 – A second DNA polymerase was discovered in E.coli by several groups in the USA and Germany (Knippers, 1970; Kornberg and Gefter, 1970; Moses and Richardson, 1970). According to the chronological order of discovery, it was named pol II. The sequencing of the polB gene was accomplished in 1990 (Chen et al., 1990) (accession P21189). 1971 – During the course of purification of E.coli pol II, a third prokaryotic DNA polymerase was detected (Kornberg and Gefter, 1971). DNA polymerase III is now known to be the main prokaryotic replicative polymerase. The dnaE gene encoding the catalytic α-subunit of pol III was sequenced in 1987 (Tomasiewicz and McHenry, 1987) (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 (Baril et al., 1971; Berger et al., 1971; Chang and Bollum, 1971; Haines et al., 1971; Weissbach et al., 1971). 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 (Zmudzka et al., 1986) (accession P06766). 1974 – A formal 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 (Weissbach et al., 1975). According to the established nomenclature, 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 (Bolden et al., 1977). 1976 – The first nuclear polymerase containing an associated 3′→5′ exonuclease activity was purified and called pol δ (Byrnes et al., 1976). 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 (Boulet et al., 1989) (accession P15436). 1987 – 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 (Jung et al., 1987). 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 (Ito and Braithwaite, 1991). In 1999 family D- was proposed to group polymerases involved in the DNA replication machinery of the Euryarchaeota (Cann and Ishino, 1999). 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 (Ohmori et al., 2001). 1989 – The fourth nuclear DNA polymerase in mammalian cells, pol ε, was first reported as a PCNA-independent form of pol δ (Focher et al., 1989). 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 (Morrison et al., 1990) (accession P21951). 1996 – Saccharomyces cerevisiae DNA pol ζ was characterized as a complex of Rev3 and Rev7 proteins (Nelson et al., 1996b). 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 (Morrison et al., 1989) (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 (Nelson et al., 1996a) that was known at the time to be required for the damage-induced mutagenesis and having ~25% identity with the E.coli UmuC protein (Larimer et al., 1989) (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. 1998 – The first evidence suggesting that the E. coli UmuD’2C complex consisting of the umuDC gene products (Perry et al., 1985; Kitagawa et al., 1985) (accession P04152), is a DNA polymerase was demonstrated (Tang et al., 1998). 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 (Tang et al., 1999). 1999 –The S.cerevisiae RAD30 gene which was previously identified by sequence homology to prokaryotic UmuC and DinB in 1996 (Kulaeva et al., 1996; McDonald et al., 1997) was shown to encode DNA polymerase η (Johnson et al., 1999b). Shortly thereafter, human polymerase η was characterized (Masutani et al., 1999b). Polη became one of the founding members of the new Y-family of DNA polymerases (Ohmori et al., 2001). Nonsense, or frameshift mutations in the gene (RAD30A, POLH, XPV) encoding pol η are responsible for the Xeroderm Pigmentosum Variant syndrome in humans (Johnson et al., 1999a; Masutani et al., 1999b). - 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 (Wagner et al., 1999). This polymerase became known as E.coli DNA pol IV. The dinB gene was originally identified as dinP in 1995 (Ohmori et al., 1995) (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. 2000 –The TLS activity of two eukaryotic Y-family polymerases ι (Tissier et al., 2000b) and κ (Ohashi et al., 2000a) (products of the POLI (RAD30B) and POLK (DINB1) genes, respectively) was demonstrated a year after they were cloned (Gerlach et al., 1999; McDonald et al., 1999) [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 (Garcia-Diaz et al., 2000) (the sequence was first submitted in 1998 (Blanco, 1998) [accession number CAB65241]), pol μ (Dominguez et al., 2000) (accession CAB65075), and pol σ (Wang et al., 2000) (first sequenced in 1995 (Sadoff et al., 1995) accession P53632). It should be noted that the DNA polymerase activity of pol σ has been contested by Haracska et al., (Haracska et al., 2005b), who suggest that the protein is actually a poly-A RNA polymerase, rather than a bona fide DNA polymerase. 2003 – 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 θ (Seki et al., 2003) and pol ν (Marini et al., 2003). It worth mentioning that pol θ, 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 (Harris et al., 1996; Sharief et al., 1999; Sonnhammer and Wootton, 1997) (accession numbers AAB67306 and AAC33565). The polymerase was originally named pol η (Burtis and Harris, 1997), but was later renamed pol θ (Burgers et al., 2001). Pol ν was sequenced in 2003 (Marini et al., 2003) (accession NP_861524). 2013 – An ability to replicate both damaged and undamaged DNA templates was detected in PrimPol, an enzyme belonging to the archaeal-eukaryotic primase superfamily (Bianchi et al., 2013; García-Gómez et al., 2013). The gene encoding PrimPol was first sequenced in 2005 (Iyer et al., 2005) (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 (Clark et al., 2016).