bims-replis Biomed News
on Replisome
Issue of 2025–05–25
nine papers selected by
Anna Zawada, International Centre for Translational Eye Research
  1. Compact Origins and Where to Find Them: ORC's Guide to Genome-Wide Licensing.
  2. USP37 prevents unscheduled replisome unloading through MCM complex deubiquitination.
  3. Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.
  4. How Shelterin Orchestrates the Replication and Protection of Telomeres.
  5. Biological activity of Arabidopsis flap endonuclease 1 (FEN1) is modulated by nuclear factors that inhibit its aggregation.
  6. Biochemical Impact of p300-Mediated Acetylation of Replication Protein A: Implications for DNA Metabolic Pathway Choice.
  7. Tumor molecular signatures: bridging the bench and the operating room.
  8. Extreme multivalency and a composite short linear motif facilitate PCNA-binding, localisation and abundance of p21 (CDKN1A).
  9. A Genetic Twist: Cytologic Evaluation of Pancreatic Adenocarcinoma and Steatohepatitic Hepatocellular Carcinoma in a Patient With a Rare POLE Mutation.
  1. Bioessays. 2025 May 19. e70018
    Compact Origins and Where to Find Them: ORC's Guide to Genome-Wide Licensing.
    Christian Speck, Luitpold Maximilian Reuter.
      Origin licensing is the first step in the fundamental process of DNA replication, which ensures the accurate transmission of an organism's genetic information. Studies in budding yeast have provided crucial insights into replication origins, revealing sequence-specific features and structural DNA elements guiding helicase loading. Here, we review the recent advances in our understanding of DNA replication origin licensing, focusing on insights into origin architecture and advancements in high-resolution sequencing. Progress in the field demonstrates that origins are compact units that load an individual MCM2-7 double hexamer, which in turn causes steric occlusion of the origin recognition complex (ORC) binding site. We discuss why, in addition to the DNA sequence, DNA shape, DNA flexibility, and correct spacing of A- and B2-elements are crucial for efficient helicase loading. These recent findings provide a mechanistic explanation for the regulation of genome-wide origin licensing and reveal fundamental principles of MCM2-7 helicase loading.
    Keywords:  ChIP‐Exo; DNA licensing; DNA replication; MCM2‐7; ORC; budding yeast; origins
    DOI:  https://doi.org/10.1002/bies.70018
  2. Nat Commun. 2025 May 16. 16(1): 4575
    USP37 prevents unscheduled replisome unloading through MCM complex deubiquitination.
    Derek L Bolhuis, Dalia Fleifel, Thomas Bonacci, Xianxi Wang, Brandon L Mouery, Jeanette Gowen Cook, Nicholas G Brown, Michael J Emanuele.
      The CMG helicase (CDC45-MCM2-7-GINS) unwinds DNA as a component of eukaryotic replisomes. Replisome (dis)assembly is tightly coordinated with cell cycle progression to ensure genome stability. However, factors that prevent premature CMG unloading and replisome disassembly are poorly described. Since disassembly is catalyzed by ubiquitination, deubiquitinases (DUBs) represent attractive candidates for safeguarding against untimely and deleterious CMG unloading. We combined a targeted loss-of-function screen with quantitative, single-cell analysis to identify human USP37 as a key DUB preventing replisome disassembly. We demonstrate that USP37 maintains active replisomes on S phase chromatin and promotes normal cell cycle progression. Proteomics and biochemical assays revealed USP37 interacts with the CMG complex to deubiquitinate MCM7, antagonizing replisome disassembly. Significantly, USP37 protects normal epithelial cells from oncoprotein-induced replication stress. Our findings reveal USP37 to be critical to the maintenance of replisomes in S phase and suggest USP37-targeting as a potential strategy for treating malignancies with defective DNA replication control.
    DOI:  https://doi.org/10.1038/s41467-025-59770-7
  3. Nat Commun. 2025 May 23. 16(1): 4782
    Modelling POLG mutations in mice unravels a critical role of POLγΒ in regulating phenotypic severity.
    Samantha Corrà, Alessandro Zuppardo, Sebastian Valenzuela, Louise Jenninger, Raffaele Cerutti, Sirelin Sillamaa, Emily Hoberg, Katarina A S Johansson, Urska Rovsnik, Sara Volta, Pedro Silva-Pinheiro, Hannah Davis, Aleksandra Trifunovic, Michal Minczuk, Claes M Gustafsson, Anu Suomalainen, Massimo Zeviani, Bertil Macao, Xuefeng Zhu, Maria Falkenberg, Carlo Viscomi.
      DNA polymerase γ (POLγ), responsible for mitochondrial DNA replication, consists of a catalytic POLγA subunit and two accessory POLγB subunits. Mutations in POLG, which encodes POLγA, lead to various mitochondrial diseases. We investigated the most common POLG mutations (A467T, W748S, G848S, Y955C) by characterizing human and mouse POLγ variants. Our data reveal that these mutations significantly impair POLγ activities, with mouse variants exhibiting milder defects. Cryogenic electron microscopy highlighted structural differences between human and mouse POLγ, particularly in the POLγB subunit, which may explain the higher activity of mouse POLγ and the reduced severity of mutations in mice. We further generated a panel of mouse models mirroring common human POLG mutations, providing crucial insights into the pathogenesis of POLG-related disorders and establishing robust models for therapeutic development. Our findings emphasize the importance of POLγB in modulating the severity of POLG mutations.
    DOI:  https://doi.org/10.1038/s41467-025-60059-y
  4. Cold Spring Harb Perspect Biol. 2025 May 19. pii: a041685. [Epub ahead of print]
    How Shelterin Orchestrates the Replication and Protection of Telomeres.
    Titia de Lange.
      Efforts to determine how telomeres solve the end-protection problem led to the discovery of shelterin, a conserved six-subunit protein complex that specifically binds to the long arrays of telomeric TTAGGG repeats at vertebrate chromosome ends. The mechanisms by which shelterin prevents telomeres from being detected as sites of DNA damage and how shelterin prevents inappropriate DNA repair pathways are now largely known. More recently, shelterin has emerged as a central player in solving the second major problem at telomeres: how to complete the duplication of telomeric DNA. This end-replication problem results from the inability of the canonical DNA replication machinery to maintain the DNA at chromosome ends. Shelterin solves this problem by recruiting two enzymes that can replenish the lost telomeric repeats: telomerase and CST-Polα/primase. How shelterin accomplishes these critical tasks is reviewed here.
    DOI:  https://doi.org/10.1101/cshperspect.a041685
  5. BMC Plant Biol. 2025 May 16. 25(1): 648
    Biological activity of Arabidopsis flap endonuclease 1 (FEN1) is modulated by nuclear factors that inhibit its aggregation.
    Arkadiusz Borek, Piotr Bonarek, Ewa Kowalska, Agnieszka Katarzyna Banaś, Wojciech Strzałka.
      Flap endonuclease 1 (FEN1) is part of a group of nuclear enzymes involved in eukaryotic DNA replication and repair. In our studies, using both biochemical and biophysical approaches, we demonstrated that Arabidopsis thaliana FEN1 (AtFEN1) is unstable and prone to aggregation. To understand the reasons for AtFEN1 aggregation, we first analyzed the effects of heparin sodium and sodium chloride on its aggregation. We found that both heparin sodium and sodium chloride modulated the aggregation of this enzyme; however, achieving the same level of aggregation inhibition required using a sodium chloride concentration five orders of magnitude higher than that of heparin. Subsequently, to identify potential nuclear factors that may modulate the biological activity of AtFEN1 in vivo, we used DNA. Our experiments showed that negatively charged double-stranded DNA (dsDNA), similarly to the double-flap DNA (dfDNA) substrate of AtFEN1, inhibited AtFEN1 aggregation. This inhibitory effect was much less pronounced when single-stranded DNA (ssDNA) was used. Moreover, dfDNA prevented the loss of biological activity of AtFEN1. Finally, we revealed that AtFEN1 aggregation was also blocked by Arabidopsis proliferating cell nuclear antigen 1 (PCNA1), a natural interacting protein of AtFEN1. However, this effect was observed only when the putative PCNA-interacting protein (PIP)-box sequence was present in AtFEN1.
    Keywords:   Arabidopsis thaliana ; Cell proliferation; DNA replication and repair; Protein aggregation
    DOI:  https://doi.org/10.1186/s12870-025-06671-y
  6. J Biol Chem. 2025 May 17. pii: S0021-9258(25)02100-3. [Epub ahead of print] 110250
    Biochemical Impact of p300-Mediated Acetylation of Replication Protein A: Implications for DNA Metabolic Pathway Choice.
    Onyekachi Ononye, Sneha Surendran, Tripthi Battapadi, Pamela VanderVere-Carozza, Olivia K Howald, Athena Kantartzis-Petrides, Matthew R Jordan, Diana Ainembabazi, Marc S Wold, John J Turchi, Lata Balakrishnan.
      Replication Protein A (RPA), a single-stranded DNA (ssDNA) binding protein, is vital for various aspects of genome maintenance such as replication, recombination, repair and cell cycle checkpoint activation. Binding of RPA to ssDNA protects it from degradation by cellular nucleases, prevents secondary structure formation and suppresses illegitimate recombination. In our current study, we identified the acetyltransferase p300 to be capable of acetylating the 70kDa subunit of RPA in vitro and within cells. The acetylation status of RPA changes throughout the cell cycle, increasing during the S and G2/M phases, and after UV-induced damage. Furthermore, we were able to specifically identify RPA directly associated with the replication fork during the S phase and UV damage to be acetylated. Based on these observations, we evaluated the impact of lysine acetylation on the biochemical properties of RPA. Investigation of binding properties of RPA revealed that acetylation of RPA increased its binding affinity to ssDNA compared to unmodified RPA. The improvement in binding efficiency was a function of DNA length with the greatest increases observed on shorter length ssDNA oligomers. Enzymatic assays further revealed that upon acetylation RPA governs the switch between the short and long flap pathway for Okazaki fragment processing. Our findings demonstrate that p300-dependent, site-specific acetylation enhances RPA's DNA binding properties, potentially regulating its function during various DNA transactions.
    Keywords:  G1/S phase; Replication Protein A (RPA); UV-induced damage; lysine acetylation; p300; single-strand DNA binding
    DOI:  https://doi.org/10.1016/j.jbc.2025.110250
  7. Am J Surg. 2025 May 07. pii: S0002-9610(25)00215-6. [Epub ahead of print]246 116393
    Tumor molecular signatures: bridging the bench and the operating room.
    Iakovos N Nomikos, Christos Kosmas, Vasiliki Gkretsi.
      Contemporary diagnostic and therapeutic strategies for many solid tumors rely on understanding the Mismatch Repair (MMR) system, a fundamental DNA repair mechanism responsible for correcting errors introduced during DNA replication. Pathology reports written for tumors excised in surgery, often indicate the expression status of MMR proteins. This is of significant clinical value, as loss of MMR protein expression is associated with the accumulation of DNA replication errors. The MMR system recognizes and replaces mismatched nucleotides, particularly in microsatellite regions. These are short, repetitive non-coding DNA sequences prone to replication errors. When MMR proteins are inactivated by genetic or epigenetic alterations, MMR deficiency (dMMR) occurs, preventing repair and leading to microsatellite instability (MSI). MSI is a hallmark of Lynch syndrome, which is commonly associated with colorectal cancer (CRC) and endometrial cancer. This work highlights the clinical utility of MMR protein and MSI status as molecular signatures and discusses diagnostic, prognostic, and therapeutic implications. Understanding these molecular changes supports clinicians in making informed therapeutic decisions and may improve patient outcomes by providing personalized treatments to fit individual tumor profiles.
    DOI:  https://doi.org/10.1016/j.amjsurg.2025.116393
  8. FEBS J. 2025 May 20.
    Extreme multivalency and a composite short linear motif facilitate PCNA-binding, localisation and abundance of p21 (CDKN1A).
    Signe Simonsen, Fia B Larsen, Caroline K Søgaard, Nicolas Jonsson, Kresten Lindorff-Larsen, Per Bruheim, Marit Otterlei, Rasmus Hartmann-Petersen, Birthe B Kragelund.
      Cyclin-dependent kinase inhibitor 1 (CDKN1A; also known as p21) promotes cell cycle arrest and regulates DNA replication and DNA repair by high-affinity binding to proliferating cell nuclear antigen (PCNA) using a C-terminal short linear motif (SLiM). High-affinity binding to PCNA is driven by positively charged flanking regions of the SLiM, but the molecular details of their interaction as well as their roles for other p21 functions are not known. Using biophysics to study the interaction between PCNA and p21 variants with different Lys/Arg compositions in the flanking regions, as well as using D-amino acids, we find that the flanking regions of p21 bind to PCNA likely through an interaction driven by complementary charges without specific contacts. Although the exact Lys/Arg composition of the p21 flanking regions is unimportant for high-affinity PCNA binding, these positions are conserved in p21 orthologs, implying a conserved biological function. Accordingly, in cell-based experiments, we find that, while the flanking regions affect p21 abundance, both the context and the Lys/Arg composition of the N-terminal flanking region are crucial for p21 nuclear localisation. Such integration of SLiMs into a composite SLiM may be a widespread phenomenon and complicates the separation of function and drug development.
    Keywords:  IDP; IDR; ITC; NLS; charges; conservation; degron; polyelectrolyte
    DOI:  https://doi.org/10.1111/febs.70133
  9. Diagn Cytopathol. 2025 May 21.
    A Genetic Twist: Cytologic Evaluation of Pancreatic Adenocarcinoma and Steatohepatitic Hepatocellular Carcinoma in a Patient With a Rare POLE Mutation.
    Lynn Messersmith, Areeba H Rizvi, Dina El-Rayes, Jimmie Stewart.
      Mutations in the DNA polymerase epsilon (POLE) gene are associated with an increased risk of various malignancies, including colorectal and other gastrointestinal, endometrial, ovarian, breast, and brain cancers. In extremely rare cases, POLE mutations have also been associated with pancreatic and hepatobiliary carcinomas. We present the case of an 87-year-old female with a complex medical history including multiple malignancies, who underwent endoscopic ultrasound-guided fine-needle aspirations of a pancreatic head mass and a liver lesion. Utilizing rapid on-site evaluation (ROSE) and full cytologic workup, she was ultimately diagnosed with synchronous pancreatic adenocarcinoma and the steatohepatitic variant of hepatocellular carcinoma. Given her history of multiple malignancies, she underwent genetic testing, and a rare germline POLE mutation was discovered. This case expands the phenotypic spectrum of potential POLE-associated syndromes and highlights the critical role of cytopathology in fine-needle aspiration procedures for diagnosis and management of complex oncologic cases.
    Keywords:  POLE; cytopathology; fine‐needle aspiration; hepatocellular carcinoma; pancreatic adenocarcinoma; tumor predisposition syndromes
    DOI:  https://doi.org/10.1002/dc.25488
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