Biology subjects

O'Donnell, M. E.

Publications and source records attributed to O'Donnell, M. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Redesign of energetically frustrated regions rescues function in defective T4 clamp loaders

DNA polymerase clamp loaders are AAA+ ATPases that load sliding clamps on DNA for high- speed replication. Using a platform for high-throughput mutagenesis of replication proteins in T4 bacteriophage, we carried out saturation mutagenesis of the AAA+ ATPase module of the T4 clamp loader bearing a mutation, Gln 118{lozenge}Asn (Q118N), that reduces fitness. We identified residues for which different mutations improve the fitness of the Q118N variant but are neutral in the wild-type background. These conditionally neutral "rescue hotspots" overlap with those identified earlier in another defective variant (D110C). These rescue hotspots localize to regions where the sequence is not optimal for the structure, as determined by energetic frustration analysis. We designed new sequences for three of these regions, using the protein-design algorithm ProteinMPNN. In two helical regions, several designed sequences increased the fitness of both wild-type and mutant proteins, likely due to enhanced stability. An inter-domain hinge in AAA+ module changes conformation during activation, and designs for the hinge lead to loss of fitness in the wild-type background. However, when using the active conformation as the template, designs for the hinge increase the fitness of defective variants. In contrast designs templated on the inactive conformation led to loss of fitness, suggesting that a proper conformational balance is crucial. Thus, adaptive capacity in the clamp loader resides in a network of conditionally neutral sites that enable functional tuning through shifts in stability and conformational equilibria.

biochemistry↗

bioRxiv2026

The E. coli clamp loader sharply bends DNA to load β-clamp onto small gaps

DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small ssDNA gaps--common intermediates during DNA repair--remains incompletely understood. Here, we show that the bacterial Escherichia coli DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the {beta}-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by [~]150{degrees}, promoting insertion of the 3'-dsDNA into the clamp. This DNA-bending mechanism allows efficient {beta}-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair. In briefZheng et al. show that the bacterial clamp loader DnaX-complex uses a DNA-bending mechanism--rather than DNA unwinding--to load the {beta}-clamp at nicks and small gaps, revealing a clamp-loading strategy distinct from eukaryotic RFC and relevant to DNA damage repair. HighlightsO_LIThe bacterial DnaX clamp loader lacks a stable shoulder DNA-binding site C_LIO_LIUnlike eukaryotic RFC, DnaX does not unwind DNA at nicks and small gaps C_LIO_LIThe E. coli {beta}-clamp contains a conserved external DNA-binding site absent in PCNA C_LIO_LISharp DNA bending enables {beta}-clamp loading at nicks and small ssDNA gaps C_LI

biochemistry↗

bioRxiv2025

Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA

The eukaryotic DNA damage and replication stress checkpoint is initiated by activation of the apical kinase complex ATR-ATRIP on RPA-coated ssDNA. In Saccharomyces cerevisiae, the Mec1-Ddc2 (hATR-ATRIP) activator and checkpoint mediator Dpb11 (hTopBP1) is recruited to the 9-1-1 checkpoint clamp (another Mec1-Ddc2 activator) at 5 ss-dsDNA junctions. It remains unclear how Mec1-Ddc2 encounters its activators on damaged DNA due to their differential DNA binding preferences. Using real-time single-molecule imaging, we show that Dpb11 binds to ssDNA directly and localizes to ss-dsDNA junctions in an RPA-dependent manner. Furthermore, Dpb11 recruits Mec1-Ddc2 to ss-dsDNA junctions. Single-molecule force spectroscopy was used to demonstrate that Dpb11 forms bridges on ssDNA, both alone and in the presence of RPA, reducing the end-to-end distance of gapped DNA. These data support a model in which Dpb11 facilitates Mec1-Ddc2 colocalization with its activators directly by recruiting Mec1-Ddc2 to gap junctions and indirectly by decreasing the effective gap length.

biophysics↗

bioRxiv2025

A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis

The ring-shaped sliding clamp PCNA enables DNA polymerases to perform processive DNA synthesis during replication and repair. The loading of PCNA onto DNA is catalyzed by the ATPase clamp loader RFC. Using a single-molecule platform to visualize the dynamic interplay between PCNA and RFC on DNA, we unexpectedly discovered that RFC continues to associate with PCNA after loading, contrary to the conventional view. Functionally, this clamp-loader/clamp complex is required for processive DNA synthesis by polymerase {delta} (Pol{delta}), as the PCNA-Pol{delta} assembly is inherently unstable. This architectural role of RFC is dependent on the BRCT domain of Rfc1, and mutation of its DNA-binding residues causes sensitivity to DNA damage in vivo. We further showed the FEN1 flap endonuclease can also stabilize the PCNA-Pol{delta} interaction and mediate robust synthesis. Overall, our work revealed that, beyond their canonical enzymatic functions, PCNA-binding proteins harbor non-catalytic functions essential for DNA replication and genome maintenance.

biophysics↗

bioRxiv2025

DNA polymerase α-primase can function as a translesion DNA polymerase

Replication of cellular chromosomes requires a primase to generate short RNA primers to initiate genomic replication. While bacterial and archaeal primase generate short RNA primers, the eukaryotic primase, Pol-primase, contains both RNA primase and DNA polymerase (Pol) subunits that function together to form a >20 base hybrid RNA-DNA primer. Interestingly, the DNA Pol1 subunit of Pol lacks a 3-5 proofreading exonuclease, contrary to the high fidelity normally associated with DNA replication. However, Polo and Pol{delta} synthesize the majority of the eukaryotic genome and both contain 3-5 exonuclease activity for high fidelity. None the less, even the small amount of DNA produced by Pol1 in each of the many RNA/DNA primers during chromosome replication adds up to tens of millions of nucleotides in a human genome. Thus it has been a longstanding question why Pol1 lacks a proofreading exonuclease. We show here that Pol is uniquely capable of traversing common oxidized or hydrolyzed template nucleotides and propose that Pol evolved to bypass these common template lesions when they are encountered during chromosome replication. Significance statementEukaryotic Pol-primase contains DNA polymerase (Pol1) and RNA primase subunits that together synthesize a >20 nucleotide hybrid RNA-DNA primer. Bacteria and archaea only require a dozen or less RNA residues to prime DNA synthesis. Therefore, why do eukaryotes require the additional DNA? We propose, and demonstrate here that Pol1, which lacks a proofreading 3-5 exonuclease, is capable of traversing some common template lesions produced in the normal hydrolytic and metabolic oxidative environment of cells. Thus, we hypothesize that Pol1 activity within the eukaryotic primase evolved to help replisomes bypass template damage. Bypassed damaged sites can be dealt with by repair processes after replication has occurred.

biochemistry↗

bioRxiv2025

The proofreading mechanism of the human leading strand DNA polymerase ϵ holoenzyme

Significance StatementReplicative DNA polymerases (Pol) function with a sliding clamp and their proofreading exonuclease provides high fidelity. Thus, study of the proofreading mechanism must both contain the Pol-clamp complex and generate the mismatch in situ to ensure the mismatched primer follows a physiological route from the pol to exo site. Despite numerous previous studies, none satisfy both criteria. This study on human Pol{varepsilon}-PCNA meets both criteria. Cryo-EM analysis captured proofreading intermediates that reveal an unexpected proofreading process. The primer is unwound by 6 nucleotides that scrunches to form out-of-register base pairs with the template. These findings provide new insights and calls for reevaluation of proofreading mechanisms performed without a sliding clamp or with an existing mismatch. The eukaryotic leading strand DNA polymerase epsilon is a dual function enzyme with a proofreading exonuclease site located 40 angstroms from the DNA synthesizing polymerase site. Errors in Pol epsilon proofreading can cause various mutations, including C to G transversions, the most prevalent mutation in cancers and genetic diseases. Pol epsilon interacts with all three subunits of the PCNA ring to assemble a functional holoenzyme. Despite previous studies on proofreading of several polymerases, how Pol epsilon, or any Pol complexed with its sliding clamp proofreads a mismatch generated in situ has been unknown. We show here by cryo-EM that a template/primer DNA substrate with a pre-existing mismatch cannot enter the exo site of Pol epsilon/PCNA holoenzyme, but a mismatch generated in the Pol site yields three proofreading intermediates of Pol epsilon/PCNA holoenzyme. These intermediates reveal how the mismatch is dislodged from the Pol site, how the DNA unwinds 6 base pairs and how the unpaired primer 3'-end is inserted into the exo site for cleavage. These results unexpectedly demonstrate that PCNA imposes strong steric constraints that extend unwinding and direct the trajectory of mismatched DNA, and that this trajectory is dramatically different than for Pol epsilon in the absence of PCNA. These findings suggest a physiologically relevant proofreading mechanism for the human Pol epsilon/PCNA holoenzyme.

biochemistry↗

bioRxiv2024

DNA polymerase Zeta is a robust reverse transcriptase

Cell biology and genetic studies have demonstrated that DNA double strand break (DSB) repair can be performed using an RNA transcript that spans the site of the DNA break as a template for repair. This type of DSB repair requires a reverse transcriptase to convert an RNA sequence into DNA to facilitate repair of the break, rather than copying from a DNA template as in canonical DSB repair. Translesion synthesis (TLS) DNA polymerases (Pol) are often more promiscuous than DNA Pols, raising the notion that reverse transcription could be performed by a TLS Pol. Indeed, several studies have demonstrated that human Pol {eta} has reverse transcriptase activity, while others have suggested that the yeast TLS Pol {zeta} is involved. Here, we purify all seven known nuclear DNA Pols of Saccharomyces cerevisiae and compare their reverse transcriptase activities. The comparison shows that Pol {zeta} far surpasses Pol {eta} and all other DNA Pols in reverse transcriptase activity. We find that Pol {zeta} reverse transcriptase activity is not affected by RPA or RFC/PCNA and acts distributively to make DNA complementary to an RNA template strand. Consistent with prior S. cerevisiae studies performed in vivo, we propose that Pol {zeta} is the major DNA Pol that functions in the RNA templated DSB repair pathway.

biochemistry↗

bioRxiv2023

Adaptive capacity of a DNA polymerase clamp-loader ATPase complex

The ability of mutations to facilitate adaptation is central to evolution. To understand how mutations can lead to functional adaptation in a complex molecular machine, we created a defective version of the T4 clamp-loader complex, which is essential for DNA replication. This variant, which is [~]5000-fold less active than the wildtype, was made by replacing the catalytic domains with those from another phage. A directed-evolution experiment revealed that multiple substitutions to a single negatively-charged residue in the chimeric clamp loader - Asp 86 - restore fitness to within [~]20-fold of wildtype. These mutations remove an adventitious electrostatic repulsive interaction between Asp 86 and the sliding clamp. Deep mutagenesis shows that the reduced fitness of the chimeric clamp loader is compensated for by lysine and arginine substitutions of several DNA-proximal residues in the clamp loader or the sliding clamp. Thus, the fitness decrease of the chimeric clamp loader is caused by a reduction in affinity between the clamp loader and the clamp. Our results demonstrate that there is a latent capacity for increasing affinity of the clamp loader for DNA and the sliding clamp, such that even single point mutations can readily compensate for the loss of function due to suboptimal interactions elsewhere.

biochemistry↗

bioRxiv2023

Molecular choreography of primer synthesis by the eukaryotic Pol α-primase

The eukaryotic polymerase (Pol ) is a dual-function DNA polymerase/primase complex that synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides for DNA replication. Pol is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2, with Pol1 and Pri1 containing the DNA polymerase activity and RNA primase activity, respectively, whereas Pol12 and Pri2 serve a structural role. It has been unclear how Pol hands over an RNA primer made by Pri1 to Pol1 for DNA primer extension, and how the primer length is defined, perhaps due to the difficulty in studying the highly mobile structure. Here we report a comprehensive cryo-EM analysis of the intact 4-subunit yeast Pol in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states in a 3.5 [A] - 5.6 [A] resolution range. We found that Pol is a three-lobed flexible structure. Pri2 functions as a flexible hinge that holds together the catalytic Pol1-core, and the noncatalytic Pol1 CTD that binds to Pol 12 to form a stable platform upon which the other components are organized. In the apo state, Pol1-core is sequestered on the Pol12-Pol1-CTD platform, and Pri1 is mobile perhaps in search of a template. Upon binding a ssDNA template, a large conformation change is induced that enables Pri1 to perform RNA synthesis, and positions Pol1-core to accept the future RNA primed site 50 [A] upstream of where Pri1 binds. We reveal in detail the critical point at which Pol1-core takes over the 3-end of the RNA from Pri1. DNA primer extension appears limited by the spiral motion of Pol1-core while Pri2-CTD stably holds onto the 5 end of the RNA primer. Since both Pri1 and Pol1-core are attached via two linkers to the platform, primer growth will produce stress within this "two-point" attachment that may limit the length of the RNA-DNA hybrid primer. Hence, this study reveals the large and dynamic series of movements that Pol undergoes to synthesize a primer for DNA replication.

biochemistry↗

bioRxiv2023

Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology

Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATP{gamma}S, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180{degrees} axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFCs preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.

biochemistry↗

bioRxiv2022

A novel 5' DNA binding site in RFC facilitates PCNA loading for gap DNA repair

RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases {delta} and {varepsilon}. The RFC pentamer forms a central chamber that binds 3 ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5 duplex. This 5 DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3 and 5 ends are present at a ssDNA gap, we propose that the 5 site facilitates RFCs PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5 DNA binding domain of Rfc1. We further observe that a 5 end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5-DNA site in lagging strand DNA synthesis

biochemistry↗

bioRxiv2021

Rad24-RFC loads the 9-1-1 clamp by inserting DNA from the top of a wide-open ring, opposite the mechanism of RFC/PCNA

In response to DNA damage, the ring-shaped 9-1-1 clamp is loaded onto 5 recessed DNA to arrest the cell cycle and activate the DNA damage checkpoint. The 9-1-1 clamp is a heterotrimeric ring that is loaded in S. cerevisiae by Rad24-RFC, an alternative clamp loader in which Rad24 replaces the Rfc1 subunit in the RFC1-5 clamp loader of PCNA. Unlike RFC that loads the PCNA ring onto a 3-ss/ds DNA junction, Rad24-RFC loads the 9-1-1 ring onto a 5-ss/ds DNA junction, a consequence of DNA damage. The underlying 9-1-1 clamp loading mechanism has been a mystery. Here we report two 3.2-[A] cryo-EM structures of Rad24-RFC bound to DNA and either a closed or 27 [A] open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. The Rad24 subunit specifically recognizes the 5-DNA junction and holds ds DNA outside the clamp loader and above the plane of the 9-1-1 ring, rather than holding DNA inside and below the clamp as in RFC. The 3 ssDNA overhang is required to obtain the structure, and thus confers a second DNA binding site. The bipartite DNA binding by Rad24-RFC suggests that ssDNA may be flipped into the open 9-1-1 ring, similar to ORC-Cdc6 that loads the Mcm2-7 ring on DNA. We propose that entry of ssDNA through the 9-1-1 ring triggers the ATP hydrolysis and release of the Rad24-RFC. The key DNA binding residues are conserved in higher eukaryotes, and thus the 9-1-1 clamp loading mechanism likely generalizes.

biochemistry↗

bioRxiv2021

ORC binds and remodels nucleosomes to specify MCM loading onto DNA

The numerous enzymes and cofactors involved in eukaryotic DNA replication are conserved from yeast to human, and the budding yeast Saccharomyces cerevisiae (S.c.) has been a useful model organism for these studies. However, there is a gap in our knowledge of why replication origins in higher eukaryotes do not use a consensus DNA sequence as found in S.c.. Using in vitro reconstitution and single-molecule visualization, we show here that S.c. origin recognition complex (ORC) stably binds nucleosomes and that ORC-nucleosome complexes have the intrinsic ability to load the replicative helicase MCM double hexamers onto adjacent nucleosome-free DNA regardless of sequence. Furthermore, we find that Xenopus laevis nucleosomes can substitute for yeast ones in engaging with ORC. Combined with new analysis of genome-wide ORC binding, our results lead us to propose that the yeast origin recognition machinery contains the cryptic capacity to bind nucleosomes near a nucleosome-free region and license origins, and that this nucleosome-directed origin licensing paradigm generalizes to all eukaryotes.

biophysics↗

bioRxiv2021

Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction

Clamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Gln 118 forms a hydrogen-bonded junction in a helical unit that we term the central coupler, because it connects the catalytic centers to DNA and the sliding clamp. A suppressor mutation indicates that hydrogen bonding in the junction is important, and molecular dynamics simulations reveal that it maintains rigidity in the central coupler. The glutamine-mediated junction is preserved in diverse AAA+ ATPases, suggesting that a connected network of hydrogen bonds that links ATP molecules is an essential aspect of allosteric communication in these proteins.

biophysics↗

bioRxiv2019

Supporting evidence for DNA shearing as a mechanism for origin unwinding in eukaryotes

Our earlier study demonstrated that head-to-head CMGs that encircle duplex DNA and track inward at origins, melt double-strand (ds) DNA while encircling the duplex by pulling on opposite strands and shearing DNA apart (Langston and ODonnell (2019) eLife 9, e46515). We show here that increasing the methylphosphonate neutral DNA from 10 nucleotides in the previous report, to 20 nucleotides, reveals that CMG encircling duplex DNA only interacts with the tracking strand compared to the non-tracking strand. This significantly enhances support that CMG tracks on duplex DNA by binding only one strand. Furthermore, EMSA assays using AMPPNP to load CMG onto DNA shows a stoichiometry of only 2 CMGs on an origin mimic DNA, containing a 150 bp duplex with two 3 prime single-strand (ss) tails, one on each end, enabling assay of dsDNA unwinding by a shearing force produced by only two head-to-head CMGs. The use of non-hydrolysable AMPPNP enabled a preincubation for CMG binding the two 3 prime tailed origin mimic DNA, and gave robust unwinding of dsDNA by head-to-head CMG-Mcm10s. With this precedent, it is possible to envision that the cell may utilize opposing dsDNA motors to unwind DNA for other types of DNA transactions besides origin unwinding.

biochemistry↗

bioRxiv2019

Ctf4 organizes sister replisomes and Pol α into a replication factory

The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol -primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol -primase into a replication factory. In the 2CMG-Ctf43-1Pol -primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol -primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.

biochemistry↗

bioRxiv2019

Single-molecule imaging of eukaryotic replisomes reveals compositional plasticity

Structural and biochemical studies have revealed the basic principles of how the replisome duplicates genomic DNA, but little is known about its dynamics during DNA replication. We reconstitute the 34 proteins needed to form the S. cerevisiae replisome and show how changing local concentrations of the key DNA polymerases tunes the ability of the complex to efficiently recycle these proteins or to dynamically exchange them. Particularly, we demonstrate redundancy of the Pol DNA polymerase activity in replication and show that Pol primase and the lagging-strand Pol {delta} can be re-used within the replisome to support the synthesis of large numbers of Okazaki fragments. This unexpected malleability of the replisome might allow it to deal with barriers and resource challenges during replication of large genomes.

biophysics↗

bioRxiv2018

Replisome preservation by a single-stranded DNA gate in the CMG helicase

The eukaryotic replicative helicase CMG is assembled at replication origins and is thought to remain topologically closed until termination. Upon encountering a lesion, CMG must vacate a stalled fork to allow DNA repair. However, the fate of CMG under these stress conditions remains unclear. Here, using correlative single-molecule fluorescence and force microscopy, we show that when uncoupled from a DNA polymerase, CMG opens a single-stranded (ss) DNA gate to traverse a forked junction and reside on double-stranded (ds) DNA. Surprisingly, CMG undergoes rapid diffusion on dsDNA and can transition back onto ssDNA for continued fork progression. The accessory protein Mcm10 is required for robust ssDNA gating. These results reveal an Mcm10-induced pathway that preserves CMG on DNA and allows it to access a repaired fork for swift replication recovery.

biophysics↗