The Principal Enzyme Involved in Dna Replication is Called

DNA Polymerases

DNA polymerase was first identified in lysates of
E.
coli
past Arthur Kornberg in 1956. The ability of this enzyme to accurately copy a Dna template provided a biochemical basis for the mode of DNA replication that was initially proposed by Watson and Crick, so its isolation represented a landmark discovery in molecular biology. Ironically, however, this first DNA polymerase to be identified (now chosen Dna polymerase I) is not the major enzyme responsible for
Due east.
coli
DNA replication. Instead, it is now clear that both prokaryotic and eukaryotic cells contain several different DNA polymerases that play distinct roles in the replication and repair of DNA.

The multiplicity of Deoxyribonucleic acid polymerases was first revealed by the isolation of a mutant strain of
E.
coli
that was deficient in polymerase I (Effigy v.1). Cultures of
E.
coli
were treated with a chemical (a mutagen) that induces a high frequency of mutations, and individual bacterial colonies were isolated and screened to identify a mutant strain lacking polymerase I. Assay of a few thousand colonies led to the isolation of the desired mutant, which was almost totally lacking in polymerase I activity. Surprisingly, the mutant bacteria grew normally, leading to the conclusion that polymerase I is not required for DNA replication. On the other mitt, the mutant bacteria were extremely sensitive to agents that damage Deoxyribonucleic acid (e.g., ultraviolet low-cal), suggesting that polymerase I is involved primarily in the repair of Dna damage rather than in Dna replication per se.

The conclusion that polymerase I is non required for replication implied that
Due east.
coli
must contain other DNA polymerases, and subsequent experiments led to the identification of two such enzymes, at present called Deoxyribonucleic acid polymerases Two and 3. The potential roles of these enzymes were investigated past the isolation of appropriate mutants. Strains of
E.
coli
with mutations in polymerase Ii were found to grow and otherwise behave normally, and so the role of this enzyme in the cell is unknown. Temperature-sensitive polymerase Three mutants, however, were unable to replicate their Deoxyribonucleic acid at high temperature, and subsequent studies have confirmed that polymerase III is the major replicative enzyme in
E.
coli.

It is now known that, in addition to polymerase 3, polymerase I is too required for replication of
E.
coli
DNA. The original polymerase I mutant was not completely defective in that enzyme, and later experiments showed that the residual polymerase I activity in this strain plays a key role in the replication process. The replication of
Due east.
coli
Deoxyribonucleic acid thus involves two singled-out Deoxyribonucleic acid polymerases, the specific roles of which are discussed below.

Eukaryotic cells comprise five DNA polymerases: α, β, γ, δ, and ε. Polymerase γ is located in mitochondria and is responsible for replication of mitochondrial DNA. The other four enzymes are located in the nucleus and are therefore candidates for involvement in nuclear DNA replication. Polymerases α, δ, and ε are nearly agile in dividing cells, suggesting that they function in replication. In contrast, polymerase β is active in nondividing and dividing cells, suggesting that it may function primarily in the repair of Deoxyribonucleic acid damage.

Two types of experiments accept provided further evidence addressing the roles of polymerases α, δ, and ε in Deoxyribonucleic acid replication. First, replication of the DNAs of some animal viruses, such every bit SV40, can be studied in cell-gratuitous extracts. The ability to report replication
in vitro
has immune direct identification of the enzymes involved, and assay of such prison cell-free systems has shown that polymerases α and δ are required for SV40 DNA replication. Second, polymerases α, δ, and ε are found in yeasts as well as in mammalian cells, enabling the utilize of the powerful approaches of yeast genetics (see Chapter three) to test their biological roles directly. Such studies betoken that yeast mutants lacking any of these three Deoxyribonucleic acid polymerases are unable to proliferate, implying a disquisitional role for polymerase ε as well as for α and δ. Even so, farther studies have shown that the essential part of polymerase ε in yeast does not require its activity as a replicative Deoxyribonucleic acid polymerase. Thus, polymerases α and δ appear to be sufficient for Deoxyribonucleic acid replication both in cell-costless systems and in yeast, then the role of polymerase ε remains to exist established.

All known Deoxyribonucleic acid polymerases share two key properties that carry disquisitional implications for Dna replication (Figure 5.2). First, all polymerases synthesize DNA just in the 5′ to 3′ direction, adding a dNTP to the 3′ hydroxyl group of a growing concatenation. 2d, Deoxyribonucleic acid polymerases tin can add together a new deoxyribonucleotide but to a preformed primer strand that is hydrogen-bonded to the template; they are non able to initiate DNA synthesis
de novo
by catalyzing the polymerization of free dNTPs. In this respect, DNA polymerases differ from RNA polymerases, which can initiate the synthesis of a new strand of RNA in the absence of a primer. As discussed later in this chapter, these properties of Dna polymerases appear disquisitional for maintaining the loftier allegiance of Dna replication that is required for cell reproduction.

The Replication Fork

Dna molecules in the procedure of replication were starting time analyzed by John Cairns in experiments in which
East.
coli
were grown in the presence of radioactive thymidine, which allowed subsequent visualization of newly replicated DNA by autoradiography (Effigy v.3). In some cases, complete circular molecules in the process of replicating could be observed. These DNA molecules contained two replication forks, representing the regions of active Deoxyribonucleic acid synthesis. At each fork the parental strands of DNA separated and 2 new daughter strands were synthesized.

The synthesis of new Deoxyribonucleic acid strands complementary to both strands of the parental molecule posed an important problem to agreement the biochemistry of DNA replication. Since the two strands of double-helical DNA run in opposite (antiparallel) directions, continuous synthesis of 2 new strands at the replication fork would require that one strand be synthesized in the 5′ to three′ direction while the other is synthesized in the reverse (3′ to five′) direction. But Deoxyribonucleic acid polymerase catalyzes the polymerization of dNTPs just in the 5′ to iii′ direction. How, and so, can the other progeny strand of Deoxyribonucleic acid be synthesized?

This enigma was resolved by experiments showing that but one strand of Dna is synthesized in a continuous mode in the direction of overall DNA replication; the other is formed from small, discontinuous pieces of DNA that are synthesized backward with respect to the direction of movement of the replication fork (Figure 5.4). These pocket-size pieces of newly synthesized DNA (chosen Okazaki fragments afterwards their discoverer) are joined by the activeness of Deoxyribonucleic acid ligase, forming an intact new Dna strand. The continuously synthesized strand is called the leading strand, since its elongation in the direction of replication fork movement exposes the template used for the synthesis of Okazaki fragments (the lagging strand).

Although the discovery of discontinuous synthesis of the lagging strand provided a mechanism for the elongation of both strands of DNA at the replication fork, it raised another question: Since Deoxyribonucleic acid polymerase requires a primer and cannot initiate synthesis
de novo, how is the synthesis of Okazaki fragments initiated? The answer is that brusque fragments of RNA serve as primers for DNA replication (Effigy five.5). In contrast to DNA synthesis, the synthesis of RNA can initiate
de novo, and an enzyme called primase synthesizes curt fragments of RNA (e.m., three to 10 nucleotides long) complementary to the lagging strand template at the replication fork. Okazaki fragments are then synthesized via extension of these RNA primers past Dna polymerase. An important consequence of such RNA priming is that newly synthesized Okazaki fragments contain an RNA-DNA joint, the discovery of which provided critical evidence for the function of RNA primers in DNA replication.

To form a continuous lagging strand of Deoxyribonucleic acid, the RNA primers must eventually be removed from the Okazaki fragments and replaced with Deoxyribonucleic acid. In
Due east.
coli, RNA primers are removed by the combined activeness of RNase H, an enzyme that degrades the RNA strand of RNA-DNA hybrids, and polymerase I. This is the aspect of
E.
coli
Dna replication in which polymerase I plays a critical part. In addition to its Dna polymerase activity, polymerase I acts as an exonuclease that tin hydrolyze DNA (or RNA) in either the 3′ to 5′ or v′ to 3′ direction. The activity of polymerase I as a 5′ to 3′ exonuclease removes ribonucleotides from the five′ ends of Okazaki fragments, assuasive them to be replaced with deoxyribonucleotides to yield fragments consisting entirely of Deoxyribonucleic acid (Effigy v.vi). In eukaryotic cells, other exonucleases accept the place of
E.
coli
polymerase I in removing primers, and the gaps between Okazaki fragments are filled by the action of polymerase δ. Every bit in prokaryotes, these DNA fragments can and then be joined by Deoxyribonucleic acid ligase.

The different DNA polymerases thus play singled-out roles at the replication fork (Figure 5.seven). In prokaryotic cells, polymerase 3 is the major replicative polymerase, functioning in the synthesis both of the leading strand of DNA and of Okazaki fragments past the extension of RNA primers. Polymerase I so removes RNA primers and fills the gaps between Okazaki fragments. In eukaryotic cells, however, two Deoxyribonucleic acid polymerases are required to do what in
E.
coli
is achieved by polymerase III alone. Polymerase α is establish in a complex with primase, and it appears to role in conjunction with primase to synthesize short RNA-Dna fragments during lagging strand synthesis. Polymerase δ can then synthesize both the leading and lagging strands, acting to extend the RNA-Dna primers initially synthesized by the polymerase α-primase complex. In add-on, polymerase δ can take the identify of
E.
coli
polymerase I in filling the gaps betwixt Okazaki fragments following primer removal.

Not but polymerases and primase only also a number of other proteins human activity at the replication fork. These additional proteins have been identified both past the analysis of
E.
coli
mutants defective in Deoxyribonucleic acid replication and past the purification of the mammalian proteins required for
in vitro
replication of SV40 Dna. 1 class of proteins required for replication binds to DNA polymerases, increasing the activeness of the polymerases and causing them to remain bound to the template Dna so that they continue synthesis of a new DNA strand. Both
East.
coli
polymerase III and eukaryotic polymerase δ are associated with two types of accessory proteins (sliding-clamp proteins and clamp-loading proteins) that load the polymerase onto the primer and maintain its stable association with the template (Figure 5.8). The clamp-loading proteins (called the γ circuitous in
East.
coli
and replication factor C [RFC] in eukaryotes) specifically recognize and bind Deoxyribonucleic acid at the junction between the primer and template. The sliding-clamp proteins (β protein in
Eastward.
coli
and proliferating cell nuclear antigen [PCNA] in eukaryotes) demark adjacent to the clamp-loading proteins, forming a ring around the template Dna. The clamp proteins and so load the Dna polymerase onto DNA at the primer-template junction. The ring formed by the sliding clamp maintains the clan of the polymerase with its template every bit replication gain, assuasive the uninterrupted synthesis of many thousands of nucleotides of DNA.

Other proteins unwind the template DNA and stabilize single-stranded regions (Figure v.ix). Helicases are enzymes that catalyze the unwinding of parental Deoxyribonucleic acid, coupled to the hydrolysis of ATP, ahead of the replication fork.
Unmarried-stranded Deoxyribonucleic acid-binding proteins
(east.thou., eukaryotic replication factor A [RFA]) so stabilize the unwound template DNA, keeping it in an extended single-stranded state and then that it can be copied by the polymerase.

Every bit the strands of parental DNA unwind, the Dna ahead of the replication fork is forced to rotate. Unchecked, this rotation would cause circular DNA molecules (such as SV40 DNA or the
East.
coli
chromosome) to become twisted effectually themselves, eventually blocking replication (Figure 5.10). This problem is solved by topoisomerases, enzymes that catalyze the reversible breakage and rejoining of Deoxyribonucleic acid strands. There are two types of these enzymes: Type I topoisomerases suspension just ane strand of Dna; type II topoisomerases introduce simultaneous breaks in both strands. The breaks introduced past type I and type II topoisomerases serve as “swivels” that permit the two strands of template DNA to rotate freely around each other then that replication can proceed without twisting the Deoxyribonucleic acid ahead of the fork (see Figure 5.10). Although eukaryotic chromosomes are composed of linear rather than circular Deoxyribonucleic acid molecules, their replication too requires topoisomerases; otherwise, the complete chromosomes would accept to rotate continually during Deoxyribonucleic acid synthesis.

Blazon II topoisomerase is needed not only to unwind DNA merely also to unravel newly replicated round Dna molecules that go interwined with each other. In eukaryotic cells, topoisomerase Two appears to be involved in mitotic chromosome condensation. In improver, studies of yeast mutants, also equally experiments in
Drosophila
and mammalian cells, betoken that topoisomerase II is required for the separation of daughter chromatids at mitosis, suggesting that it functions to untangle newly replicated loops of DNA in the chromosomes of eukaryotes.

The enzymes involved in DNA replication act in a coordinated manner to synthesize both leading and lagging strands of DNA simultaneously at the replication fork (Figure five.xi). This job is achieved past the germination of dimers of the replicative Deoxyribonucleic acid polymerases (polymerase III in
East.
coli
or polymerase δ in eukaryotes), each with its appropriate accessory proteins. 1 molecule of polymerase then acts in synthesis of the leading strand while the other acts in synthesis of the lagging strand. The lagging strand template is thought to form a loop at the replication fork so that the polymerase subunit engaged in lagging strand synthesis moves in the same overall management as the other subunit, which is synthesizing the leading strand.

The Fidelity of Replication

The accuracy of DNA replication is critical to cell reproduction, and estimates of mutation rates for a diversity of genes indicate that the frequency of errors during replication corresponds to only one incorrect base of operations per 10^nine
to 10¹⁰
nucleotides incorporated. This error frequency is much lower than would be predicted simply on the basis of complementary base pairing. In particular, the standard configurations of nucleic acrid bases are in equilibrium with rare culling conformations (tautomeric forms) that hydrogen-bond with the wrong partner (e.g., Thousand with T) with a frequency of about one wrong base per 10⁴
(Figure 5.12). The much higher degree of allegiance really achieved results largely from the activities of DNA polymerase.

One mechanism by which Dna polymerase increases the allegiance of replication is by helping to select the right base for insertion into newly synthesized Deoxyribonucleic acid. The polymerase does not simply catalyze incorporation of any nucleotide is hydrogen-bonded to the template strand. Instead, information technology actively discriminates confronting incorporation of a mismatched base, presumably by adapting to the conformation of a correct base of operations pair. The molecular mechanisms responsible for the power of Deoxyribonucleic acid polymerases to select against incorrect bases are not notwithstanding entirely understood, simply this selectivity appears to increase the accurateness of replication about a hundredfold, reducing the expected error frequency from ten^-4
to approximately 10^-six.

The other major machinery responsible for the accurateness of DNA replication is the proofreading activity of Deoxyribonucleic acid polymerase. As already noted,
E.
coli
polymerase I has iii′ to 5′ too as v′ to 3′ exonuclease activity. The 5′ to 3′ exonuclease operates in the management of DNA synthesis and helps remove RNA primers from Okazaki fragments. The 3′ to 5′ exonuclease operates in the reverse management of DNA synthesis, and participates in proofreading newly synthesized DNA (Effigy 5.13). Proofreading is constructive considering Dna polymerase requires a primer and is not able to initiate synthesis
de novo. Primers that are hydrogen-bonded to the template are preferentially used, so when an incorrect base is incorporated, it is likely to exist removed past the 3′ to 5′ exonuclease activity rather than existence used to continue synthesis. Such 3′ to 5′ exonuclease activities are also associated with
East.
coli
polymerase III and eukaryotic polymerases δ and ε. The 3′ to 5′ exonucleases of these polymerases selectively excise mismatched bases that take been incorporated at the end of a growing DNA concatenation, thereby increasing the accuracy of replication by a hundred- to a thousandfold.

The importance of proofreading may explain the fact that DNA polymerases require primers and catalyze the growth of DNA strands only in the five′ to 3′ direction. When Deoxyribonucleic acid is synthesized in the 5′ to 3′ direction, the energy required for polymerization is derived from hydrolysis of the 5′ triphosphate group of a free dNTP equally it is added to the 3′ hydroxyl group of the growing chain (see Figure 5.2). If DNA were to exist extended in the 3′ to 5′ direction, the energy of polymerization would instead have to be derived from hydrolysis of the 5′ triphosphate group of the concluding nucleotide already incorporated into Deoxyribonucleic acid. This would eliminate the possibility of proofreading, because removal of a mismatched terminal nucleotide would also remove the 5′ triphosphate group needed as an free energy source for further chain elongation. Thus, although the power of Deoxyribonucleic acid polymerase to extend a primer only in the 5′ to 3′ management appears to make replication a complicated process, it is necessary for ensuring accurate duplication of the genetic fabric.

Combined with the ability to discriminate against the insertion of mismatched bases, the proofreading activity of Dna polymerases is sufficient to reduce the error frequency of replication to about one mismatched base per 10⁹. Additional mechanisms (discussed in the section “Dna Repair”) act to remove mismatched bases that have been incorporated into newly synthesized Dna, farther ensuring correct replication of the genetic information.

Origins and the Initiation of Replication

The replication of both prokaryotic and eukaryotic DNAs starts at a unique sequence called the origin of replication, which serves as a specific bounden site for proteins that initiate the replication process. The first origin to exist divers was that of
Due east.
coli, in which genetic analysis indicated that replication ever begins at a unique site on the bacterial chromosome. The
E.
coli
origin has since been studied in detail and found to consist of 245 base pairs of DNA, elements of which serve as binding sites for proteins required to initiate Dna replication (Figure five.14). The key stride is the binding of an initiator protein to specific DNA sequences within the origin. The initiator protein begins to unwind the origin Dna and recruits the other proteins involved in Dna synthesis. Helicase and single-stranded Deoxyribonucleic acid-binding proteins then act to proceed unwinding and exposing the template DNA, and primase initiates the synthesis of leading strands. Two replication forks are formed and movement in opposite directions along the round
Eastward.
coli
chromosome.

The origins of replication of several animal viruses, such every bit SV40, have been studied every bit models for the initiation of DNA synthesis in eukaryotes. SV40 has a single origin of replication (consisting of 64 base pairs) that functions both in infected cells and in cell-complimentary systems. Replication is initiated by a virus-encoded poly peptide (called T antigen) that binds to the origin and besides acts as a helicase. A single-stranded Deoxyribonucleic acid-binding protein is required to stabilize the unwound template, and the DNA polymerase α-primase circuitous then initiates Deoxyribonucleic acid synthesis.

Although single origins are sufficient to direct the replication of bacte-rial and viral genomes, multiple origins are needed to replicate the much larger genomes of eukaryotic cells inside a reasonable period of time. For instance, the unabridged genome of
E.
coli
(four × 10⁶
base pairs) is replicated from a single origin in approximately 30 minutes. If mammalian genomes (iii × ten^ix
base pairs) were replicated from a unmarried origin at the same rate, Deoxyribonucleic acid replication would require well-nigh 3 weeks (30,000 minutes). The problem is farther exacerbated by the fact that the rate of Dna replication in mammalian cells is actually virtually tenfold lower than in
E.
coli, mayhap as a result of the packaging of eukaryotic DNA in chromatin. All the same, the genomes of mammalian cells are typically replicated within a few hours, necessitating the employ of thousands of replication origins.

The presence of multiple replication origins in eukaryotic cells was showtime demonstrated by the exposure of cultured mammalian cells to radioactive thymidine for unlike time intervals, followed by autoradiography to detect newly synthesized DNA. The results of such studies indicated that DNA synthesis is initiated at multiple sites, from which it and so gain in both directions along the chromosome (Effigy 5.fifteen). The replication origins in mammalian cells are spaced at intervals of approximately 50 to 300 kb; thus the human genome has virtually xxx,000 origins of replication. The genomes of simpler eukaryotes also have multiple origins; for case, replication in yeasts initiates at origins separated past intervals of approximately xl kb.

The origins of replication of eukaryotic chromosomes take been studied all-time in yeasts, in which they accept been identified every bit sequences that can back up the replication of plasmids in transformed cells (Effigy 5.sixteen). This has provided a functional assay for these sequences, and several such elements (called
autonomously replicating sequences,
or
ARSs) have been isolated. Their role every bit origins of replication has been verified by direct biochemical analysis, not only in plasmids only as well in yeast chromosomal DNA.

Functional ARS elements span about 100 base of operations pairs, including an 11-base-pair core sequence common to many dissimilar ARSs (Effigy v.17). This core sequence is essential for ARS function and has been found to be the binding site of a protein complex (called the origin replication complex, or
ORC) that is required for initiation of Dna replication at yeast origins. The ORC complex appears to recruit other proteins (including Dna helicases) to the origin, leading to the initiation of replication. The mechanism of initiation of DNA replication in yeasts thus appears similar to that in prokaryotes and eukaryotic viruses; that is, an initiator protein specifically binds to origin sequences.

In contrast to the well-defined ARS elements in yeasts, much less is known nigh the nature of replication origins in more complex eukaryotes. However, recent experiments have shown that specific origin sequences are required for initiation of Dna replication in mammalian cells. In improver, proteins related to the yeast ORC proteins have been identified in a variety of eukaryotes, including
Drosophila,
C. elegans,
Arabidopsis, and humans, and shown to be essential for DNA replication. It thus appears likely that the basic mechanism used to initiate DNA replication is conserved in eukaryotic cells.

Telomeres and Telomerase: Replicating the Ends of Chromosomes

Because Dna polymerases extend primers just in the v′ to 3′ direction, they are unable to re-create the extreme 5′ ends of linear Dna molecules. Consequently, special mechanisms are required to replicate the terminal sequences of the linear chromosomes of eukaryotic cells. These sequences (telomeres) consist of tandem repeats of unproblematic-sequence DNA (meet Affiliate 4). They are replicated past the activeness of a unique enzyme called telomerase, which is able to maintain telomeres by catalyzing their synthesis in the absence of a DNA template.

Telomerase is a reverse transcriptase, one of a class of Deoxyribonucleic acid polymerases, beginning discovered in retroviruses (see Chapter 3), that synthesize Deoxyribonucleic acid from an RNA template. Importantly, telomerase carries its ain template RNA, which is complementary to the telomere repeat sequences, equally part of the enzyme complex. The use of this RNA as a template allows telomerase to generate multiple copies of the telomeric repeat sequences, thereby maintaining telomeres in the absence of a conventional Deoxyribonucleic acid template to direct their synthesis.

The mechanism of telomerase action was initially elucidated in 1985 past Carol Greider and Elizabeth Blackburn during studies of the protozoan
Tetrahymena
(Figure v.18). The
Tetrahymena
telomerase is complexed to a 159-nucleotide-long RNA that includes the sequence 3′-AACCCCAAC-5′. This sequence is complementary to the
Tetrahymena
telomeric echo (5′-TTGGGG-3′) and serves as the template for the synthesis of telomeric DNA. The utilise of this RNA every bit a template allows telomerase to extend the three′ end of chromosomal Dna by one echo unit of measurement across its original length. The complementary strand can so be synthesized by the polymerase α-primase complex using conventional RNA priming. Removal of the RNA primer leaves an overhanging iii′ end of chromosomal Deoxyribonucleic acid, which tin grade loops at the ends of eukaryotic chromosomes (run across Figure 4.xix).

Telomerase has been identified in a variety of eukaryotes, and genes encoding telomerase RNAs have been cloned from
Tetrahymena, yeasts, mice, and humans. In each example, the telomerase RNA contains sequences complementary to the telomeric repeat sequence of that organism (see Table 4.3). Moreover, the introduction of mutant telomerase RNA genes into yeasts has been shown to upshot in corresponding alterations of the chromosomal telomeric repeat sequences, directly demonstrating the function of telomerase in maintaining the termini of eukaryotic chromosomes.