COMMENTARY

COMMENTARY

Solution to the 50-year-old Okazaki-

fragment problem
Peter M. Burgersa,1

The antiparallel structure of double-stranded DNA,

together with the known 5′→3′ directionality of DNA
polymerases, necessitates that the two DNA strands
are replicated in opposite directions. The leading
strand is synthesized in the same direction as the rep-
lication fork, whereas the lagging strand is replicated
in the opposite direction. In a 1968 paper in PNAS,
Reiji and Tsuneko Okazaki and colleagues (1) pro-
posed that the lagging strand is replicated discontin-
uously in the form of small fragments that subsequently
are matured into one continuous strand. A review of the
current state of molecular biology published that year
(2) named these small fragments “Okazaki fragments,”
as they have been called since. The seminal studies of
Okazaki et al. (1) generated the textbook model of the
semidiscontinuous replication fork, with a continuous
leading strand and a discontinuous lagging strand. How-
ever, their original experimental results were not in ac-
cord with this model, and their studies suggested that all Fig. 1. (A–D) Models for the possible structure and
reaction in the replicating region of DNA. Reprinted with
nascent DNA fragments are small. Was the leading
permission from ref. 1.
strand also synthesized discontinuously, as was depicted
in figure 1 of ref. 1 (Fig. 1C)? Fifty years after the landmark
paper, this question has been answered by Cronan et al. fractionated near the top of the gradient, with a
(3), who show that the leading strand is indeed replicated DNA length of 1 to 2 kb. Only a small fraction of the
continuously. However, this strand is fragmented due label appeared as a shoulder with a size of up to 10 kb,
to ribonucleotide excision repair (RER) (4, 5). RER similarly to the result shown in Fig. 2B (black curve).
removes genomic ribonucleotides that are errone- Obviously, the data supported the model in Fig. 1C
ously inserted by replicative DNA polymerases more than the idealized model in Fig. 1B for semidis-
(Fig. 2A). continuous DNA replication. These curious results
To detect the earliest lagging-strand pieces syn- were not just an E. coli oddity or artifact; they extended
thesized, before they could be matured into continu- to the gram-positive bacterium Bacillus subtilis and to
ous DNA, Okazaki et al. (1) used pulse-labeling bacteriophage T4 (7).
techniques in Escherichia coli, with 3H-thymidine Over the next few years, the Okazaki team in-
pulses as brief as 5 s. Given that the DNA replication troduced several improvements and gained more
rate is 500 to 1,000 nt/s and an average Okazaki frag- advanced knowledge of the small fragments that were
ment is 1 to 2 kb in size, it only takes a few seconds to named after them. They showed that the pulse-
synthesize a single Okazaki fragment. The pulse- labeled small fragments could be chased into large
labeled DNA was denatured and size-fractionated fragments upon addition of an excess of cold thymi-
on an alkaline sucrose gradient. Surprisingly, even dine, indicating that they were true intermediates in
though biochemical studies at the time suggested the synthesis of chromosomal DNA. They discovered
that the leading strand could be synthesized in a con- that the synthesis of Okazaki fragments is primed with
tinuous fashion (6), virtually all of the labeled DNA a short RNA primer (8). They also showed that the

a
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
Author contributions: P.M.B. wrote the paper.
The author declares no conflict of interest.
Published under the PNAS license.
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See companion article on page 1251 in issue 4 of volume 116.

1
Email: [email protected].
Published online February 15, 2019.

3358–3360 | PNAS | February 26, 2019 | vol. 116 | no. 9 www.pnas.org/cgi/doi/10.1073/pnas.1900372116

 mutant (11). The sof mutant is defective for dUTPase, which sani-
tizes the dNTP pool by hydrolyzing erroneously synthesized dUTP.
This analog is readily incorporated into DNA during DNA replica-
tion, but the uracil base is subsequently excised by uracil-DNA-
glycosylase, followed by base excision repair (BER) of the abasic
moiety. In the sof mutant, the high level of dUTP resulted in fre-
quent dUMP misincorporation and hence frequent BER, which
caused severe fragmentation of newly synthesized DNA. However,
it was also clear from these studies that uracil excision did not
contribute to the generation of short fragments in wild-type cells
(11). Nevertheless, they reinforced the notion that DNA repair
might contribute to the generation of short fragments on the lead-
ing strand. But which form of DNA repair? A mutant defective for all
forms of BER, nucleotide excision repair (NER), and mismatch repair
(MMR) still failed to show the expected bimodal distribution of sizes
for a fully semidiscontinuous DNA replication model (12).
Even before Okazaki et al. (1) published their seminal studies, it
was known that DNA polymerases could use ribonucleoside tri-
phosphates (rNTPs) as substrates, albeit poorly (13). Critical in-
sights into the nature and abundance of genomic ribonucleotides
came from studies in yeast. The replicative DNA polymerases show
a robust discrimination of 104 to 105 for dNTP versus rNTP incor-
poration (14). At first glance, this low frequency of misincorporation
should not pose a serious problem. However, the intracellular con-
centrations of the four rNTPs are 30- to 200-fold higher than those
of the corresponding dNTPs. Therefore, in a simple competition
assay, when rNTPs and dNTPs were present at their physiological
concentrations, a much more frequent misincorporation occurred,
about one ribonucleotide per kilobase (14). These genomic ribonu-
cleotides are excised by the RER pathway, which is initiated by
RNase H2-catalyzed incision at the 5′-ribonucleotide position (Fig.
2A) (4). The RER pathway is specific for RNase H2 (RnhB in E. coli),
because RNase H1 does not cut at single genomic ribonucleotides.
In E.coli, the dNTP pools are not as low as they are in yeast; nev-
ertheless, the dATP concentration is one-twentieth that of ATP (15).
It appears that ribonucleotide misinsertion could be the source of
the half-century-old leading-strand fragmentation problem.
Fig. 2. (A) DNA incision intermediates in the BER of a damaged or To carry out their analysis, Cronan et al. (3) make use of a
unnatural base (X), or the RER of a genomic ribonucleotide. Only repair temperature-sensitive ligase strain in which DNA ligase activity
on the leading strand, which leads to its fragmentation, is shown. (B) Size is shut down rapidly upon a shift from 28 to 42 °C, preventing
distribution, in a formamide-urea-sucrose gradient, of single-stranded
ligation of processed Okazaki fragments and the ligation of exci-
replication intermediates. Ligts cells were shifted to 42 °C to inactivate
ligase, and cells were pulse-labeled with 3H-thymidine for 2 min. The sion repair events. In addition, they make an important modifica-
BER− NER− MMR− defective mutant is mutY mug ung nth nei tag alkA tion to the original Okazaki protocol. Anticipating that ribonucleotides
mutM nfi uvrA mutS; the RER− defective mutant is rnhB. Curves redrawn would remain in the genome in an E. coli rnhB mutant that is defective
from ref. 3, fig. 3b. DNA size markers are approximate. E. coli Okazaki for RER, they could no longer rely on alkaline sucrose gradients for the
fragments are 1 to 2 kb.
size separation of nascent single-stranded DNA. RNA is sensitive to
alkali, and the DNA could be fragmented at ribonucleotide insertion
sites during centrifugation under alkaline conditions. Therefore, they
direction of DNA synthesis in vivo was the same as determined turned to formamide-urea-sucrose gradients carried out at neutral pH,
in vitro (i.e., 5′→3′) and that the RNA primer indeed was at the 5′ which showed a similar separatory power of denatured DNA. With this
end of an Okazaki fragment. However, despite all these improve- improvement, they first reinvestigated the size distribution of labeled
ments, the fact remained that all nascent DNA was small in size, DNA from a mutant defective in BER, NER, and MMR (Fig. 2B, brown
begging the question regarding the exact nature of leading- curve). Compared with the isogenic wild-type strain, the higher-
strand DNA replication. After the untimely death of Reiji Okazaki molecular-weight shoulder on the peak of Okazaki-size products had
in 1975, Tsuneko continued the groundbreaking studies that she shifted slightly to the left, indicative that some repair of newly repli-
and her husband had initiated at Nagoya University. Her team cated DNA occurred. However, products larger than ∼50 kb in size
determined the structures of the RNA primers in prokaryotes were absent. Remarkably, the profile from an rnhB mutant showed a
and eukaryotes (9). Tsuneko Okazaki’s recent account of their bimodal distribution of product sizes, with the high-molecular-weight
studies of replication intermediates can be found in ref. 10. products centered around 50 kb (Fig. 2B, blue curve). Finally, when all
The first indication that DNA repair might be responsible for repair mutations were combined, a robust high-molecular-weight dis-
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some of the small fragments detected in pulse-labeling studies tribution was observed, centered around 80 kb (Fig. 2B, green curve).
came from the study of an E. coli sof (for short Okazaki fragment) Importantly, >90% of the small fragments mapped to the lagging

Burgers PNAS | February 26, 2019 | vol. 116 | no. 9 | 3359

 strand, and 90% of the large DNA mapped to the leading strand. remains as to how continuous. Replication forks tend to stall
These data are consistent with an earlier study by Okazaki et al. for a variety of reasons, and cells have several mechanisms to
(16), in which a mutation in DNA polymerase I caused a defect in restart replication forks (17). Some of these restart mecha-
the joining of all small nascent fragments, because E. coli DNA nisms use the available 3′ terminus for restart, after recom-
polymerase I is required for RER as well as Okazaki fragment bination or fork remodeling, but a de novo restart by RNA
maturation (5). priming is also a possible mechanism. The latter would show
The new study by Cronan et al. (3) shows that the incorporation up as a fragmentation event on the leading strand. In their
of ribonucleotides and their subsequent excision by RER is a fre- study of the size distributions of leading strands in the multiple-
quent event. Cronan et al. assess the frequency of this event by pathway excision repair-defective strain (RER− BER− NER− MMR−),
measuring the number of ribonucleotides present in a plasmid Cronan et al. (3) provide evidence that, indeed, the leading
propagated in an rnhB strain. From the fraction of the isolated strand is not completely continuous. Whether these disconti-
plasmid that was nicked by RNase H2 and using the reasonable nuities are the result of still another repair pathway, the result
assumption that ribonucleotide insertion is random, Cronan et al. of replication-fork restart, or the result of the stochastic, unpro-
use the Poisson equation to calculate the misinsertion frequency voked activity of DNA primase on the leading strand needs
at one ribonucleotide per 8 to 9 kb, or about 500 per genome. By further investigation.
1 order of magnitude, RER in bacteria appears to be the most
Acknowledgments
frequently employed DNA repair pathway, as it is in eukaryotes. I thank Andrei Kuzminov and colleagues for sharing their results prior to publi-
While it is evident from the current study that the leading cation. This research is supported by the National Institutes of Health Grant R35-
strand is synthesized largely continuously, the question still GM118129.

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3360 | www.pnas.org/cgi/doi/10.1073/pnas.1900372116 Burgers