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Replicative DNA Polymerases

Erik Johansson1 and Nicholas Dixon2

1Department of Medical Biochemistry and Biophysics, Umea˚ University, SE-90187 Umea˚, Sweden 2School of Chemistry, University of Wollongong, NSW 2522, Australia Correspondence: [email protected]; [email protected]

In 1959, Arthur Kornberg was awarded the Nobel Prize for his work on the principles by which DNA is duplicated by DNA polymerases. Since then, it has been confirmed in all branches of life that replicative DNA polymerases require a single-stranded template to build a complementary strand, but they cannot start a new DNA strand de novo. Thus, they also depend on a primase, which generally assembles a short RNA primer to provide a 30-OH that can be extended by the replicative DNA polymerase. The general principles that (1) a heli- case unwinds the double-stranded DNA, (2) single-stranded DNA-binding proteins stabilize the single-stranded DNA, (3) a primase builds a short RNA primer, and (4) a clamp loader loads a clamp to (5) facilitate the loading and processivity of the replicative polymerase, are well conserved among all species. Replication of the genome is remarkably robust and is performed with high fidelity even in extreme environments. Work over the last decade or so has confirmed (6) that a common two-metal ion-promoted mechanism exists for the nucleo- tidyltransferase reaction that builds DNA strands, and (7) that the replicative DNA poly- merases always act as a key component of larger multiprotein assemblies, termed replisomes. Furthermore (8), the integrity of replisomes is maintained by multiple protein–protein and protein–DNA interactions, many of which are inherently weak. This enables large confor- mational changes to occur without dissociation of replisome components, and also means that in general replisomes cannot be isolated intact.

he genomes, from the smallest to the larg- BUILDING DNA Test, provide an enormous challenge for the replicative DNA polymerases to faithfully copy Considerable progress in the description of the to give the many generations that follow a chemical and structural basis for DNA synthesis comparable condition for life. In this article, has been made in recent years. A large variety of we discuss the structural and functional bases DNA polymerases have been isolated and stud- by which replicative DNA polymerases are ied since the initial discovery of Escherichia coli able to efficiently and faithfully build new cop- DNA Pol I. The DNA polymerases have been ies of genomes in eubacteria, archaea, and eu- divided into families based on homology of karyotes. their primary sequences. The replicative DNA

Editors: Stephen D. Bell, Marcel Me´chali, and Melvin L. DePamphilis Additional Perspectives on DNA Replication available at www.cshperspectives.org Copyright # 2013 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a012799 Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012799

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E. Johansson and N. Dixon

polymerases from eukarya are found in family domains for 30 –50 exonucleolytic proofreading, B, bacteria in families A and C, and archaea in interactions with other proteins, or other func- families B and D. The structures of the catalytic tions. subunits of these polymerases share a similar Both the growing DNA and template organization, and the nucleotidyl transferase strands are integral components of their active reaction of adding nucleotides to the 30-OH of sites, providing information about which nu- the growing strand is conserved (Table 1). All cleotide should be added, and the 30-hydroxyl known structures of DNA polymerases (exam- group acts as a nucleophile to attack the a phos- ples in Fig. 1) appear to resemble a right hand, phate of the correct incoming deoxyribonu- where the functional domains are depicted as cleoside triphosphate (dNTP). This all occurs fingers, palm, and thumb domains, and the rep- in the palm domain, which is the most highly licative polymerases often contain additional conserved subdomain. Here, two magnesium

Table 1. A current view of subunit compositions and roles of subunits of replicative DNA polymerases Eubacteria Firmicutes Human Yeast (Sc) Yeast (Sp) (Eury)archaea (Eco) (Bsu) Chromosomal Pol d (d) and Pol d (d) and Pol d (d) and Pol B (B) Pol III HE Pol C replicases Pol 1 (1) Pol 1 (1) Pol 1 (1) Pol D (D) (DnaE þ nine other subunits) Replicase (d): PolD1/ (d): Pol3/ (d): Pol3/ (B): Pol B a1u Pol C core(s) PolD2/ Pol31/ Cdc1/ (D): (DP1/ PolD3/ Pol32 Cdc27/ DP2)2 PolD4 (1): Pol2/ Cdm1 (1): Pol E/ Dpb2/ (1): Pol2/ PolE2/ Dpb3/ Dpb2/ PolE3/ Dpb4 Dpb3/ PolE4 Dpb4 Polymerase (d): PolD1 (d): Pol3 (d): Pol3 (B): Pol B a (DnaE) Pol C subunit (1): Pol E (1): Pol2 (1): Pol2 (D): DP2 Proofreading (d): PolD1 (d) Pol3 (d): Pol3 (B): Pol B 1 (DnaQ) Pol C subunit (1): Pol E (1) Pol2 (1): Pol2 (D): DP1 Primase Pol a (Prim1/ Pol a (Pri1/ Pol a (Pri1/ PriSL DnaG DnaG (subunits) Prim2A) Pri2) Spp2) Primer Pol a (PolA1/ Pol a (Pol1/ Pol a (Pol1/ DnaE/ extension Pol2A) Pol12) Pol12) DnaQ (subunits) Leading-strand Pol 1 Pol 1 Pol 1 Pol B a1u Pol C Pol Lagging-strand Pol d Pol d Pol d Pol B or Pol D a1u Pol C Pol (?) Clamp PCNA PCNA PCNA PCNA b b 0 00 Clamp loader RFC RFC RFC RFC t2gdd xc t3dd (pentamer (pentamer (pentamer (pentamer of of five of five of five two different different different different subunits) subunits) subunits) subunits) Okazaki Pol d/FEN1/ Pol d/FEN1/ Pol d/FEN1/ FEN1 Pol I Pol I fragment PCNA, PCNA, PCNA, processing Dna2 Dna2 Dna2 Isolable complexes are color coded. PCNA, proliferating cell nuclear antigen; RFC, replication factor C.

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Replicative DNA Polymerases

AB1T7P 3IAY C2HNH Bacteriophage T7 gp43 Saccharomyces cerevisiae Pol δ Escherichia coli Pol III Family A Family B Family C

Amino-terminal domain Exonuclease domain Divalent metal ions

Palm PHP domain Incoming nucleotide

Fingers β-Binding domain DNA

Thumb

Figure 1. Representative structures and domain architecture of DNA polymerases from the A, B, and C families. (A) Bacteriophage T7 gene 5 protein with primer-template DNA (family A; pdb 1T7P). (Data from Doublie´ et al. 1998.) (B) Saccharomyces cerevisiae Pol d (family B; pdb 3IAY). (Data from Swan et al. 2009.) (C) E. coli Pol III a subunit, residues 1–917 (family C; pdb 2HNH). (Data from Lamers et al. 2006.) Figure drawn using PyMOL.

ions are coordinated by two invariable aspartic also contacts the duplex DNA (Bailey et al. 2006; acids. This is the basis for the two-metal cata- Lamers et al. 2006; Wing et al. 2008). lyticmechanism(Steitz1993),conservedamong Replicative DNA polymerases are highly ac- all replicative polymerases studied so far. The curate during the synthesis of DNA. In addition fingers domain is adjacent to the palm domain, they have either a built-in 30 –50 exonuclease contacts the incoming nucleotide, and goes site, located at a distance from the polymerase through large conformational changes when active site, or an associated subunit with 30 –50 the nucleotide is positioned near the metals, exonuclease activity (reviewed in Patel and Loeb template, and the 30 end of the growing strand 2001; Kunkel 2004; McHenry 2011). In either in the active site (Yang et al. 1999; Franklin et al. case, the distance from the polymerase site to the 2001). The thumb domain, which interacts with exonuclease site necessitates that at least three the duplex DNA upstream of the polymerase nucleotides of the double-stranded DNA are active site, has been shown in A- and B-family unwound to allow editing. This is a particularly polymerases to influence the partitioning be- important facet of the editing function because tween editing and polymerization modes (Dou- the exonuclease sites only accommodate single- blie´ et al. 1998; Franklin et al. 2001). Mutations stranded DNA. in the thumb domain can act both as antimu- At every replication fork, replicative poly- tators and mutators, depending on how the bal- merasescooperateincopyingbothDNAstrands. ance has been shifted either toward the editing Because the directions of the two template or the polymerization mode (Stocki et al. 1995; strands are opposite, and polymerases can only Wu et al. 1998). The thumb domain in C-fami- extend preexisting primers from their 30-OH ly polymerases may have a similar function to end, only one strand can be made continuously that in A- and B-family polymerases, because it (the leading strand). The other (lagging) strand

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E. Johansson and N. Dixon

has to be synthesized in the direction opposite replisome, and they are thus isolated in as- the fork movement as a series of short (Oka- semblies that contain fewer accessory subunits. zaki) fragments that are processed and subse- We will discuss here the core catalytic subunit quently joined together. In general, leading- and accessory subunits that are considered to be and lagging-strand synthesis is coordinated, but parts of the DNA polymerase. how this is achieved varies somewhat among or- ganisms. Eubacteria Replicases from all domains of life function within larger molecular machines called repli- Pol III holoenzyme is the E. coli chromosomal somes that contain helicase(s), which separate replicase that synthesizes both leading and lag- the two DNA strands at the apex of the replica- ging strands simultaneously. As isolated directly tion fork, a primase for repeated RNA priming from cells, it has an average composition close 0 in lagging-strand synthesis, sliding clamps that to (a1u)2 –(t2gdd cx)–(b2)2 (17 subunits), encircle the nascent double-stranded product to where a1u is the polymerase core discussed in tether polymerases onto the DNA to ensure they more detail below, b2 is the sliding clamp, and 0 dissociate rarely, clamp loaders that load the t2gdd cx is the clamp loader complex that may clamps, various single-stranded DNA-binding contain two to three t and one to zero g sub- proteins, etc. The ring-shaped sliding clamps, units (McHenry 2011). called the b subunit (a homodimer) in eubac- The a1u core of Pol III is a tightly associated teria and PCNA (a homotrimer) in archaea and complex. The large a subunit is a family C po- eukaryotes, have very similar structures (Kong lymerase, and 1 is a separate 30 –50 editing exo- et al. 1992; Krishna et al. 1994). They interact nuclease subunit from the DnaQ family. The at the same site in each of their subunits with small u subunit has a role in stabilizing 1, but many other proteins including the replicative it only occurs in a limited range of bacterial polymerases, via short peptide motifs called species. The a subunit is made up of a series the clamp-binding motif in eubacteria (Dal- of domains (Fig. 1C) (Bailey et al. 2006; Lamers rymple et al. 2001) and the PIP box in higher et al. 2006): the amino-terminal PHP domain organisms (Warbrick 1998). The structures and seems to be a vestigial exonuclease domain that functions of the sliding clamps and other ac- may still be functional as a proofreader in some cessory replisomal components are described species (Stano et al. 2006). In E. coli, it has in detail in the literature. evolved to be the site of interaction of the 1 sub- So far we have highlighted a few well-con- unit (Wieczorek and McHenry 2006). This do- served features of the replicative polymerases. main is followed by the usual polymerase palm, However, as we now proceed with a more de- thumb, and fingers domains, and a b-binding tailed comparison, you will find that they have domain that contains a conserved clamp-bind- special features to function in their specific en- ing motif that interacts with the b2 clamp to vironments. tether a to the product DNA to ensure its high processivity. This is followed by an OB-fold domain that is likely to interact with the sin- QUATERNARY STRUCTURE gle-stranded template DNA, and a carboxy- The quaternary structures of replicative poly- terminal domain that interacts tightly with merases vary significantly (Table 1). In part, the carboxy-terminal domain of the t subunit this variation rather arbitrarily depends on of the clamp loader. Because the clamp loader which subunits are isolated together to define contains two (or three) t subunits, at least two the polymerase. From some species (e.g., Pol III a1u cores are maintained in the replicase com- in Escherichia coli [Eco]), a holoenzyme can be plex, one each for leading- and lagging-strand purified as an entity with 10 different subunits. synthesis. In eukaryotes, the replicative polymerases ap- The 1 subunit has a globular amino-ter- pear to be more loosely associated within the minal exonuclease domain (residues 7–180),

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Replicative DNA Polymerases

the structure of which is reminiscent of many primer synthesis on both the leading and lag- editing exonuclease domains from other poly- ging strands. merases (Hamdan et al. 2002). It contains a There is no crystal structure available of a binuclear metal site for processing nucleotides complete Pol III core from any bacterium, but misincorporated by a, followed by a poorly available structures of a subunits include E. coli conserved63-residuecarboxy-terminalsegment a(1–917), which misses its internal clamp- that by itself is unstructured. The last 40 res- binding motif and domains that follow it idues are now known to be involved directly (Lamers et al. 2006), and full-length Thermus in binding to the PHP domain of a (Ozawa et aquaticus (Taq) a (DnaE), both by itself and al. 2008); a short segment that immediately fol- in complex with primer-template DNA (Bailey lows the exonuclease domain contains a second et al. 2006; Wing et al. 2008). The most recent clamp-binding motif (S Jergic and N Dixon, structure is of a ternary complex containing unpubl.), and the unstructured segment in be- primer-template DNA and incoming dNTP tween remains flexible even in the a1u complex bound to Pol C from Geobacillus kaustophilus (Ozawa et al. 2008). This may suggest an unusu- (Gka) (Evans et al. 2008). The Taq and Eco struc- al mechanism in which 1 can occupy quite dif- tures without DNA are very similar in the re- ferent positions in the complex when it is or is gions that can be compared (Fig. 1C), but DNA not being used for proofreading. binding induces large conformational changes Most (or all) eubacterial species seem to to a closed state, especially in the b-binding have replicase subunits closely related to a region of the Taq protein. The Gka Pol C terna- (DnaE family) and 1, but some Gram-positive ry complex is also similar to the Taq a–DNA bacteria like Bacillus subtilis (Bsu) also have a structure in this respect. Interestingly, the struc- second more distantly related polymerase/exo- ture of a b2 –DNA complex (Georgescu et al. nuclease called Pol C (Table 1). These latter en- 2008a) can be docked neatly into both the zymes have the proofreading and polymerase a and Pol C–DNA structures to give plausible activities in a single polypeptide, and a different models of the a or Pol C–b2 –DNA replicases domain organization, with putative t-binding in the polymerization mode (Evans et al. 2008; and OB-fold domains preceding a discontinu- Wing et al. 2008), and it has been suggested that ous PHP domain that incorporates the proof- the open structures might mimic the replicase reader, and the b-binding motif being right structure in the editing mode (Fig. 2A). The at the carboxyl terminus (Evans et al. 2008). position of the proofreading exonuclease has Although it was for some time believed that not been defined (it was deleted from the Pol C Pol C was dedicated to leading-strand synthe- construct used for crystallization), but it is pre- sis and DnaE to the lagging strand (Dervyn et sumably between the PHP domains and b2 in al. 2001), recent work suggests that most chro- the modeled structures. A second interesting as- mosomal DNA synthesis in these bacteria is pect of the a/Pol C structures is that the palm performed by Pol C. However, because only domain (active site) architecture is distinct from the DnaE polymerase can extend RNA primers that found in the A- and B-family polymerases, like those made by the DnaG primase, it has a being closer to that of X family members like the critical role in lagging-strand synthesis. The cur- eukaryotic repair polymerase, Pol b. This sug- rent model is that DnaE extends RNA primers gests that the replicative polymerases of eubac- for some length before passing them to Pol C teria evolved independently of those in eukary- (Sanders et al. 2010). This has some parallel otes and archaea. with the eukaryotic Pol a (below). Note that The other polymerase that plays a significant in eubacteria, RNA priming is performed by a role in bacterial DNA replication is Pol I, the dedicated primase (DnaG) that does not as- founding member of the family A polymer- sociate directly with the polymerase; it is asso- ases (representative Pol A structure is shown in ciated, sometimes firmly and often more tran- Fig. 1A). Its primary function in replication is in siently, with the replicative helicase to enable Okazaki fragment processing on the lagging

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E. Johansson and N. Dixon

A Pol C 3′–5′ exonuclease 3′–5′ exonuclease ssDNA ssDNA 5′ ′ 5 Pol IV

Pol

30° 30°

β β -Binding β-Clamp -Binding Exo/TLS motif motif β-Clamp

B Pol B Exonuclease Exonuclease Polymerase active site Polymerase active site active site active site

PIP

PIP

PCNA

PCNA

Polymerization mode Proofreading mode

Figure 2. Modeled structures of ternary complexes of polymerases, clamps, and DNA in the polymerization and editing modes. (A) Geobacillus kaustophilus Pol C with DNA and b sliding clamp. (Panel A is from Evans et al. 2008; reprinted, with express permission, from the authors.) (B) Pyrococcus furiosus Pol B with DNA and PCNA (Mayanagi et al. 2011). (Panel B is from Mayanagi et al. 2011; reprinted, with permission, from The National Academy of Science # 2011.)

strand. Pol III is capable of synthesizing Okazaki proofreading exonuclease used to ensure high fragments right up to the 50 end of a preceding fidelity. Thus, Pol I uses a process of “nick trans- RNA primer, whereupon it is recycled to a new lation” to replace RNA primers with DNA, leav- primer terminus, leaving behind a nick or short ing a nick with a 30-OH and 50-phosphate that is gap (discussed in Dohrmann et al. 2011). Pol I a substrate for DNA ligase, which seals the nick has three separate activities in a single polypep- to make a contiguous lagging strand. tide chain. The amino-terminal domain is a 50 –30 exonuclease capable of excising the RNA primers at the same time as the carboxy-termi- Archaea nal polymerase domain (with thumb, palm, and The replisome in archaebacteria is less com- fingers subdomains) extends the DNA primer plex than in eubacteria, and in most aspects is behind it. The central domain is a DnaQ family a simplified version of the eukaryotic system.

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Replicative DNA Polymerases

All archaea contain single-subunit Pol B poly- the template DNA ahead of the polymerase for merases, with the proofreading activity includ- the uracil base in dUMP produced by cytosine ed in the catalytic subunit as a domain near the deamidation (and hypoxanthine, from adeno- amino terminus (Table 1). Some genera have sine) that has escaped repair by uracil-N-glyco- multiple Pol Bs (family B), whose separate roles sylase (Greagg et al. 1999, Fogg et al. 2002). On in chromosomal replication are yet to be clear- recognition of dUMP in the template, the poly- ly defined, whereas the euryarchaea uniquely merase stalls four nucleotides before the lesion also contain a more complex heterotetrameric is encountered. Although how this might lead Pol D polymerase, with subunit composition to subsequent repair of the lesion is not known, (DP1)2 –(DP2)2. The smaller DP1 subunit con- crystal structures have been reported of stalled tains a 30 –50 exonuclease domain, whereas the complexes containing primer templates with larger DP2 is the (family D) polymerase. Al- appropriately incorporated dUMP or dIMP though Pol D is a processive and efficient en- (Firbank et al. 2008, Killelea et al. 2010). The zyme that, in common with Pol B, also interacts bases are buried within a specific pocket in the with the PCNA sliding clamp, the role of Pol D amino-terminal domain, and the primer-tem- as a chromosomal replicase in euryarchaeal spe- plate DNA is thought to be in a position in the cies is still uncertain (Tori et al. 2007). It has structure close to that in the editing mode, by been suggested that in Pyrococcus abyssi, Pol B comparison to the RB69 Pol B structure (Frank- synthesizes the leading and Pol D the lagging lin et al. 2001). strand (Henneke et al. 2005). High-resolution In a recent study (Mayanagi et al. 2011), structural information on Pol D is limited to the a series of available crystal structures was com- crystal structure of the amino-terminal domain bined with low-resolution reconstructions from of Pyrococcus horikoshii DP2, which has a role electron microscopy and single-particle analy- in Pol D subunit oligomerization (Matsui et al. sis to generate plausible models of the structures 2011). of archaeal Pol B–DNA–clamp ternary com- The crenarchaea do not have Pol Ds, but of- plexes in both the polymerization and proof- ten have multiple Pol Bs. Forexample, Sulfolobus reading modes (Fig. 2B). As for the bacterial solfataricushasthreeofthem,andPol B1(Dpo1) Pol III complex (Fig. 2A), these models generate is a high-fidelity polymerase thought to carry new hypotheses that will be tested in the future, out both leading- and lagging-strand replication leading to further progressive improvement of (Choi et al. 2011). The archaeal Pol Bs have been our understanding of replisome structure and studiedextensively,inpartbecausesomeofthem function. from thermophilic species are used extensively A significant difference between the archae- for high-fidelity PCR applications. Although al replisomes and those in eukaryotes (see be- crystal structures of Pol Bs from several archaeal low) is that archaea, like the bacteria, use pri- species have been determined (the earliest are in mases that are not physically associated with Hopfner et al. 1999, Zhao et al. 1999, Rodriguez the polymerases. Nevertheless, the archaeal pri- et al. 2000, and Hashimoto et al. 2001), there is mases contain two subunits (p41 and p46) that noneyet that showsprimer-templateDNA in the are homologs of the PriS and PriL subunits of polymerization or proofreading modes. These the eukaryotic Pol a–primasecomplex(Table1). structures can, however, be modeled using the Recent in vitro studies with purified proteins structures of the T4-related phage RB69 Pol B, have shown quite clearly that the Thermococcus bound to DNA in both of these modes (Franklin kodakarensis primase can carry out (DNA) pri- et al. 2001). mer synthesis in the total absence of ribonu- The archaeal Pol Bs seem generally and cleoside triphosphates (rNTPs), and in a roll- uniquely among family B polymerases (Wardle ing-circle assay with a synthetically primed et al. 2008) to contain an additional amino- minicircle DNA template, it can prime efficient terminal domain that precedes the proofreading lagging-strand Okazaki-fragment synthesis de- exonuclease domain, whose function is to scan pendent on the hexameric MCM replicative

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E. Johansson and N. Dixon

helicase and Pol B (Chemnitz Galal et al. 2012). Chilkova et al. 2007). The exact roles of Pols 1 Thus, the stage is now set to use in vitro studies and d at the replication fork have been debated with the archaeal replisome to probe mechanis- (Kunkel and Burgers 2008; Burgers 2009). Over tic questions in the way that has already been the pastfewyears,evidencehasaccumulated that performed with the model bacterial systems. in S. cerevisiae and Schizosaccharomyces pombe (Sp), Pol 1 is primarily responsible for leading- strand and Pol d for lagging-strand synthesis Eukarya (Pursell et al. 2007; Nick McElhinny et al. 2008; Eukaryotes have evolved a more complex repli- Miyabe et al. 2011). This suggests that the roles some that depends on three different B-fami- of Pol 1 and Pol d are evolutionarily conserved ly DNA polymerases: Pol a,Pold, and Pol 1 among eukaryotes. (Kunkel and Burgers 2008; Burgers 2009). Each Pol d is constituted of three subunits (Pol3, of these multisubunit polymerases (Table 1) has Pol31, and Pol32) in S. cerevisiae, and four in one catalytic core subunit and two to four ac- S. pombe and H. sapiens (Table 1) (Gerik et al. cessory subunits. Pol a is built up by four differ- 1998; Reynolds et al. 1998; Liu et al. 2000). This ent subunits: PriS, PriL, Pol1, and Pol12 (Muzi- may be species variations but could also reflect Falconi et al. 2003); PriL has primase activity how tightly specific subunits are associated with and Pol1 has DNA polymerase activity. Nega- the catalytic core subunit. The hydrodynamic tive-stain EM reconstructions combined with properties of ScPol d and SpPol d suggested high-resolution structures of domains of the that Pol d has an elongated structure, heavily Saccharomyces cerevisiae (Sc) Pol1–Pol12 com- influenced by the Pol32 subunit (Johansson plex have revealed two globular domains con- et al. 2001; Bermudez et al. 2002). This was later nected via a flexible linker (Klinge et al. 2009). It confirmed by small-angle X-ray scattering was suggested that an intramolecular hand-off (SAXS) analysis of ScPol3 in complex with occurs from the primase domain to the poly- Pol31 and the amino terminus of Pol32 and a merase domain when the initial RNA primer high-resolution structure of the human acces- has reached a specific length (Klinge et al. 2009; sory subunits Pold2 together with the amino Nunez-Ramirez et al. 2011). The final result is a terminus of Pold3 (Baranovskiy et al. 2008; 30–35 nucleotide primer with RNA at the 50 Jain et al. 2009). The catalytic subunit ScPol3 end and DNA at the 30 end. Thus, Pol a synthe- is located at one end of the complex; Pol31 acts sizes a substantial amount of DNA because the as a bridge to the very elongated Pol32 that car- eukaryotic Okazaki fragments are on average ries an important interaction motif with PCNA only about 165 nucleotides long (Smith and at the far end of the elongated structure ex- Whitehouse 2012). Thus, the absence of a proof- tending away from the catalytic core subunit reading activity in Pol a requires that errors Pol3 (Johansson et al. 2004; Baranovskiy et al. made by it are corrected by other mechanisms. 2008; Jain et al. 2009). A high-resolution struc- For instance Pol d, but not Pol 1, proofreads ture of ScPol3 (amino acid residues 68–985) errors made by Pol a, in addition to error cor- was solved which included both the exonuclease rection by the mismatch repair system (Pavlov and polymerase domains (Fig. 1B), but exclud- et al. 2006; Nick McElhinny et al. 2010a). ed the carboxy-terminal domain with the CysA Pol 1 and Pol d are responsible for the bulk and CysB motifs discussed below. Overall, the synthesis of DNA on the leading and lag- structure of ScPol3 is highly reminiscent of a ging strands (Kunkel and Burgers 2008; Burgers typical family B polymerase, with a fold very 2009). They are both highly accurate DNA po- similar to that of RB69 despite the limited se- lymerases with built-in 30 –50 exonuclease ac- quence identity (Swan et al. 2009). tivities for proofreading (Morrison et al. 1991; Pol 1 consists of four subunits. In S. cerevi- Morrison and Sugino 1994). They are also high- siae, these are called Pol2, Dpb2, Dpb3, and ly processive enzymes when interacting with Dpb4 (Hamatake et al. 1990; Chilkova et al. the clamp, PCNA (Burgers 1991; Lee et al. 1991; 2003). Structural information on Pol 1 is limited

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Replicative DNA Polymerases

to a low-resolution cryo-electron microscopy (Baranovskiy et al. 2012) and it remains to be (cryo-EM) structure. ScPol 1 has two domains, shown whether the ScPols a and 1 holoenzymes a globular domain with the catalytic subunit carry Fe–S clusters that mediate the interactions and an extended tail domain that has been sug- between the catalytic subunit and Pol12 and gested to harbor the three accessory subunits Dpb2, respectively. The study of the carboxy- Dpb2, Dpb3, and Dpb4 (Asturias et al. 2006). terminal domain of the catalytic subunit in hu- Dpb2 is essential in S. cerevisiae and S. pombe man Pol d confirmed that there is an Fe–S center (Araki et al. 1991; Feng et al. 2003). However, the coordinated by CysB (Baranovskiy et al. 2012). Dpb2 subunit does not appear to influence the As discussed above, ScPol d has at least polymerase activity in human Pol 1 (Bermudez two well-defined motifs that mediate the con- et al. 2011). It is possible that the essential func- tact with PCNA. Two additional motifs, one in tion of Dpb2 is during the initiation of DNA Pol3 and one in Pol31, were recently reported, replication, as described in Tanaka and Araki emphasizing that ScPol d has multiple surfaces (2013) (also reviewed in Araki 2010). Dpb3 to stabilize the interactionwith PCNAwhen syn- and Dpb4 form a heterodimer that has a high thesizing DNA (Acharya et al. 2011). Less is affinity for double-stranded DNA (Tsubotaet al. known about how Pol 1 interacts with PCNA. 2006). In contrast to Dpb2, ScPol 1 depends on In S. cerevisiae, the catalytic subunit and Dpb2 Dpb3 and Dpb4 for full processivity in the ab- both have a PIP box, but they are not located at sence of PCNA (Aksenova et al. 2010). the amino or carboxyl terminus as found typi- The eukaryotic replicative polymerases all cally in PCNA-interacting proteins (Dua et al. have two conserved motifs with cysteines (CysA 2002). Biochemical characterizations and ge- and CysB) located at the carboxyl terminus of netic experiments in yeast suggested that these the catalytic subunit (Netz et al. 2012). For a are not functional motifs during DNA replica- long time they have been considered to be Zn- tion (Dua et al. 2002; Chilkova et al. 2007). Nev- finger motifs and Zn was found in both Pol 1 ertheless, Pol 1 is stimulated by PCNA in vitro, and Pol a (Dua et al. 2002; Klinge et al. 2009). suggesting that either the exact motif(s) remains Their primary role was suggested to form an to be found or there are multiple weak interac- interaction surface with the B subunit of the tions that together stabilize the interaction with DNA polymerase. Recently it was shown that PCNA (Maga et al. 1999). Pol 1 also has an un- the two motifs CysA and CysB have differential usually high intrinsic processivity in part medi- functions and coordinate different metals in ated by the Dpb3 and Dpb4 subunits (Aksenova ScPol d (Netz et al. 2012). CysA coordinates Zn et al. 2010). In addition, the catalytic subunit has and is required to support processive synthesis by itself an unusually high processivity and it by Pol d via a direct interaction with PCNA, was speculated that a 66 amino acid insertion whereas CysB coordinates a Fe–S center and is in the vicinity of the palm domain might give important for the interaction with the Pol31 Pol 1 this unusual property (Shcherbakova subunit. Loss of interaction with Pol31 led to et al. 2003). loss of Pol32, and as a result an important in- teraction with the PCNA clamp was lost. Thus, FIDELITY OF THE REPLICATIVE Pol d has at least two separate interactions with POLYMERASES PCNA, CysA in Pol3 and the PIP box in Pol32, to support efficient loading and synthesis of The high fidelity of replicative polymerases is DNA (Netz et al. 2012). Experiments with car- determined by the tolerance for the incoming boxy-terminal domains of Pol a and Pol 1 im- nucleotide when performing chemistry and the plied that these replicative polymerases may also 30 –50 exonucleolytic proofreading activity. In have an Fe–S cluster. However, conflicting re- addition, the concentration of each dNTP in the sults with expression of the carboxy-terminal cell and the quality of the template influence the domains of the catalytic subunits from human rate at which errors are made (Kunkel 2011). Pols a and 1 in E. coli were recently published Until recently, not much attention was paid to

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E. Johansson and N. Dixon

how the relatively large pools of rNTPs in eu- ANTIBIOTICS/INHIBITORS karyotic cells influence the fidelity of the rep- licative DNA polymerases. The polymerases DNA replication is an essential process in all have a built-in steric gate that should select for organisms. Although there are sufficient varia- dNTPs and against rNTPs (Joyce 1997). How- tions in structures among replisomal proteins ever, the concentration of dNTPs is very low in from bacteria and humans to make replisomes a comparison to the rNTPs and it appears that very good target for discovery of new antibacte- Pols a, d, and 1 misincorporate ribonucleotides rial therapeutics, it is a target that is surprisingly at a surprisingly high rate when synthesizing underexploited both by pharmaceutical compa- DNA (Nick McElhinny et al. 2010c). All three nies and in nature by other organisms (reviewed Pols also incorporated rNTPs in vivo in S. cer- in Robinson et al. 2010, 2012). Although there evisiae and S. pombe and gave a significantly are no known inhibitors of DnaE-type Pol IIIs, increased elevation of 2–5 nucleotide deletions there have been substantial effortsto target Pol C (Nick McElhinny et al. 2010b; Miyabe et al. from Gram-positive bacteria, including Staph- 2011). To avoid mutagenic events, ribonucleo- ylococcus aureus, using a range of 6-anilinoura- tides must be removed by a repair mechanism cils (6-AUs) and quinazolin-2-ylamino-quina- that involves RNase H2 before the next S phase zolin-4-ols (BisQuinols). The 6-AUs act as Pol C (Nick McElhinny et al. 2010b; Miyabe et al. inhibitors by competing with dGTP for base 2011). The incorporation of ribonucleotides pairing with cytosines in the template DNA, and the dependence on RNase H2 for the re- whereas the BisQuinols appear to interfere moval of ribonucleotides was also found in with template DNA binding. Another promis- mice, suggesting that this repair mechanism is ing target is the b clamp, which makes essential conserved among all eukaryotes (Reijns et al. interactions with the clamp-binding motifs in 2012). The exact mechanism behind the error a large number of other proteins (including all signature in S. cerevisiae is unknown, but Pol a, five DNA polymerases, the clamp loader, and Pol d, and Pol 1 stall when encountering a ri- DNA ligase in E. coli, for example) at a single bonucleotide in the template and this may lead highly conserved binding site that is structurally to deletions in repetitive sequences (Watt et al. distinct from the PIP-binding sites in PCNA 2011). In case ribonucleotides are not removed, (Dalrymple et al. 2001). Development of resis- postreplication repair will be activated during tance to antibacterials that inhibit interactions the next S phase (Lazzaro et al. 2012). Pol z is at this site by target mutagenesis would be ex- capable of replicating across 1–4 ribonucleo- pected to be slow because it would require si- tides in the template and also MMS2-depen- multaneous mutations to arise in genes encod- dent template switching contributes to the tol- ing several different proteins. There have been erance for unrepaired ribonucleotide lesions recent reports of identification through screen- (Lazzaro et al. 2012). ing campaigns of new inhibitors of interactions It is yet unclear if archaeal DNA polymer- with b, including two crystal structures (Geor- ases also frequently misinsert ribonucleotides in gescu et al. 2008b; Wijffels et al. 2011), but there the genome. However, as described earlier, the is much to be done to develop these compounds archaeal replicative polymerases (in, e.g., P. fur- into useful leads. iosus and S. solfataricus) have a unique capacity to proofread the template for uracil and other CONCLUDING REMARKS deamidated bases (Greagg et al. 1999; Choi et al. 2011). A binding pocket for uracil is found in Almost 60 years have passed since the first iso- their unique amino-terminal domains where lation of a replicative DNA polymerase by Ar- the single-stranded template is scanned before thur Kornberg in the mid-1950s. In this long entering the polymerase catalytic site (Fogg history of research, many modern tools in struc- et al. 2002; Shuttleworth et al. 2004; Firbank tural and molecular biology have provided frag- et al. 2008). ments of information for progressive synthesis

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of coherent pictures of how these complex mul- yeast DNA polymerase d modulate its function in DNA tifunctional enzymes work in organisms from replication. Proc Natl Acad Sci 108: 17927–17932. Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, all three domains of life. There are common as- Kunkel TA, Pavlov YI, Johansson E. 2010. Mismatch re- pects that are well established, like the common pair—Independent increase in spontaneous mutagenesis catalytic mechanism of the nucleotidyltrans- in yeast lacking non-essential subunits of DNA polymer- ferase reaction, but our pictures are still far from ase 1. PLoS Genet 6: e1001209. Araki H. 2010. Cyclin-dependent kinase-dependent initia- complete. The main reason for this is that these tion of chromosomal DNA replication. Curr Opin Cell enzymes never work alone. They are key parts Biol 22: 766–771. of larger, very dynamic nucleoprotein mach- Araki H, Hamatake RK, Johnston LH, Sugino A. 1991. ines (replisomes) that undergo large structural DPB2, the gene encoding DNA polymerase II subunit B, is required for chromosome replication in Saccharo- changes as they function, with proteins coming myces cerevisiae. Proc Natl Acad Sci 88: 4601–4605. and going and often changing binding partners. Asturias FJ, Cheung IK, Sabouri N, Chilkova O, Wepplo D, Sometimes this occurs at common binding sites Johansson E. 2006. Structure of Saccharomyces cerevisiae (as on the sliding clamps) to ensure ordered se- DNA polymerase epsilon by cryo-electron microscopy. Nat Struct Mol Biol 13: 35–43. quences of events, and often interactions involve Bailey S, Wing RA, Steitz TA. 2006. The structure of intrinsically unstructured regions of proteins T. aquaticus DNA polymerase III is distinct from eukary- that only become ordered as they interact with otic replicative DNA polymerases. Cell 126: 893–904. their binding partners. This latter fact alone has Baranovskiy AG, Babayeva ND, Liston VG, Rogozin IB, Koonin EV, Pavlov YI, Vassylyev DG, Tahirov TH. 2008. made structural studies slow and difficult, and it X-ray structure of the complex of regulatory subunits of also means that multiple structures need to be human DNA polymerase d. Cell Cycle 7: 3026–3036. solved to really understand function. A second Baranovskiy AG, Lada AG, Siebler HM, Zhang Y, Pavlov YI, basic operating principle for replisomes is that Tahirov TH. 2012. DNA polymerase d and z switch by sharing accessory subunits of DNA polymerase d. J Biol their integrity is maintained by a very large Chem 287: 17281–17287. number of protein–protein and protein–nu- Bermudez VP, MacNeill SA, Tappin I, Hurwitz J. 2002. The cleic acid interactions, many of which are inher- influence of the Cdc27 subunit on the properties of the ently weak and can easily be transiently broken. Schizosaccharomyces pombe DNA polymerase d. J Biol These interactions are often difficult to detect Chem 277: 36853–36862. Bermudez VP, Farina A, Raghavan V, Tappin I, Hurwitz J. individually, but sum to be strong enough to 2011. Studies on human DNA polymerase 1 and GINS hold the replisomes together as they function. complex and their role in DNA replication. J Biol Chem 286: 28963–28977. Burgers PM. 1991. Saccharomyces cerevisiae replication fac- ACKNOWLEDGMENTS tor C. II. Formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymer- We apologize to those colleagues whose work ases d and 1. J Biol Chem 266: 22698–22706. is not cited because of formatting and space Burgers PM. 2009. Polymerase dynamics at the eukaryotic restrictions. We thank Matthew Hogg for help DNA replication fork. J Biol Chem 284: 4041–4045. Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. 2012. with Figure 1, and Rick Lewis for comments on Characterization of DNA primase complex isolated the manuscript. Research in our laboratories from the archaeon, Thermococcus kodakearaensis, J Biol is funded by the Swedish Cancer Society, the Chem 287: 16209–16219. Swedish Research Council, the Knut and Alice Chilkova O, Jonsson BH, Johansson E. 2003. The quaternary structure of DNA polymerase 1 from Saccharomyces cer- Wallenberg foundation (E.J.), the Australian evisiae. J Biol Chem 278: 14082–14086. Research Council, including an Australian Pro- Chilkova O, Stenlund P, Isoz I, Stith CM, Grabowski P, fessorial Fellowship, and the Australian Nation- Lundstrom EB, Burgers PM, Johansson E. 2007. 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Replicative DNA Polymerases

Erik Johansson and Nicholas Dixon

Cold Spring Harb Perspect Biol 2013; doi: 10.1101/cshperspect.a012799

Subject Collection DNA Replication

Replication of Epstein−Barr Viral DNA Endoreplication Wolfgang Hammerschmidt and Bill Sugden Norman Zielke, Bruce A. Edgar and Melvin L. DePamphilis Replication Proteins and Human Disease Replication-Fork Dynamics Andrew P. Jackson, Ronald A. Laskey and Karl E. Duderstadt, Rodrigo Reyes-Lamothe, Nicholas Coleman Antoine M. van Oijen, et al. Break-Induced DNA Replication Helicase Activation and Establishment of Ranjith P. Anand, Susan T. Lovett and James E. Replication Forks at Chromosomal Origins of Haber Replication Seiji Tanaka and Hiroyuki Araki Regulating DNA Replication in Eukarya Poxvirus DNA Replication Khalid Siddiqui, Kin Fan On and John F.X. Diffley Bernard Moss Archaeology of Eukaryotic DNA Replication The Minichromosome Maintenance Replicative Kira S. Makarova and Eugene V. Koonin Helicase Stephen D. Bell and Michael R. Botchan Translesion DNA Polymerases DNA Replication Origins Myron F. Goodman and Roger Woodgate Alan C. Leonard and Marcel Méchali Human Papillomavirus Infections: Warts or Principles and Concepts of DNA Replication in Cancer? Bacteria, Archaea, and Eukarya Louise T. Chow and Thomas R. Broker Michael O'Donnell, Lance Langston and Bruce Stillman Chromatin and DNA Replication DNA Replication Timing David M. MacAlpine and Geneviève Almouzni Nicholas Rhind and David M. Gilbert

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