bims-replis 2025-07-06 papers

Nat Struct Mol Biol. 2025 Jun 30.

Mechanisms for licensing origins of DNA replication in eukaryotic cells.

Bruce Stillman, John F X Diffley, Janet H Iwasa.

The initiation of DNA replication in eukaryotic cells begins with the assembly of pre-replicative complexes (pre-RCs) at many sites along each chromosome during the G1 phase of the cell cycle. Pre-RCs license each chromosome for duplication during S phase and mark the origins of DNA replication. In this Review, we discuss and contextualize recent findings identifying the mechanisms of origin recognition and pre-RC assembly mediated by the origin recognition complex (ORC), Cdc6 and the Mcm2-Mcm7 (Mcm2-7) hexamer bound to Cdt1. We also present comprehensive videos that demonstrate the multiple mechanisms for pre-RC assembly and compare the structures of the complexes involved in human and Saccharomyces cerevisiae cells.

DOI: https://doi.org/10.1038/s41594-025-01587-5

Nat Commun. 2025 Jul 01. 16(1): 5502

BAHCC1 binds H4K20me1 to facilitate the MCM complex loading and DNA replication.

Dongxu Li, Zhi-Min Zhang, Liu Mei, Yao Yu, Yiran Guo, Samuel G Mackintosh, Jianbin Chen, David F Allison, Arum Kim, Aaron J Storey, Ricky D Edmondson, Stephanie D Byrum, Alan J Tackett, Ling Cai, Jeanette G Cook, Jikui Song, Gang Greg Wang.

Mono-methylation of histone H4 lysine 20 (H4K20me1) regulates DNA replication, cell cycle progression and DNA damage repair. How exactly H4K20me1 regulates these biological processes remains unclear. Here, we report that an evolutionarily conserved tandem Tudor domain (TTD) in BAHCC1 (BAHCC1TTD) selectively reads H4K20me1 for facilitating replication origin activation and DNA replication. Our biochemical, structural, genomic and cellular analyses demonstrate that BAHCC1TTD preferentially recognizes H4K20me1 to promote the recruitment of BAHCC1 and its interacting partners, notably Mini-chromosome Maintenance (MCM) complex, to replication origin sites. Combined actions of the H4K20me1-reading BAHCC1 and the H4K20me2-reading Origin Recognition Complex (ORC) ensure genomic loading of MCM for replication. Depletion of BAHCC1, or disruption of the BAHCC1TTD:H4K20me1 interaction, reduces H4K20me1 levels and MCM loading, leading to defects in replication origin activation and cell cycle progression. In summary, this study identifies BAHCC1TTD as an effector transducing H4K20me1 signals into MCM recruitment to promote DNA replication.

DOI: https://doi.org/10.1038/s41467-025-61284-1

Nat Struct Mol Biol. 2025 Jun 30.

Cell cycle regulation has shaped replication origins in budding yeast.

Chew Theng Lim, Thomas C R Miller, Kang Wei Tan, Saurabh Talele, Anne Early, Philip East, Humberto Sánchez, Nynke H Dekker, Alessandro Costa, John F X Diffley.

Eukaryotic DNA replication initiates from genomic loci known as origins. At budding yeast origins like ARS1, a double hexamer (DH) of the MCM replicative helicase is assembled by origin recognition complex (ORC), Cdc6 and Cdt1 by sequential hexamer loading from two opposed ORC binding sites. Cyclin-dependent kinase (CDK) inhibits DH assembly, which prevents re-replication by restricting helicase loading to the G1 phase. Here, we show that an intrinsically disordered region (IDR) in the Orc2 subunit promotes interaction between ORC and the first loaded, closed-ring MCM hexamer (the MCM-ORC (MO) intermediate). CDK-dependent phosphorylation of this IDR blocks MO formation and DH assembly. We show that MO stabilizes ORC at lower-affinity binding sites required for second hexamer loading. Origins comprising two high-affinity ORC sites can assemble DH efficiently without MO by independently loading single hexamers. Strikingly, these origins escape CDK inhibition in vitro and in vivo. Our work reveals mechanistic plasticity in MCM loading with implications for understanding how CDK regulation has shaped yeast origin evolution and how natural, strong origins might escape cell cycle regulation. We also identify key steps common to loading pathways, with implications for understanding how MCM is loaded in other eukaryotes.

DOI: https://doi.org/10.1038/s41594-025-01591-9

Nucleic Acids Res. 2025 Jun 20. pii: gkaf521. [Epub ahead of print]53(12):

DnaB and DciA: mechanisms of helicase loading and translocation on ssDNA.

Nicholas Gao, Daniele Mazzoletti, Adele Peng, Paul Dominic B Olinares, Castrese Morrone, Andrea Garavaglia, Nourelhoda Gouda, Sergey Tsoy, Albert Mendoza, Ahammad Chowdhury, Antonio Cerullo, Hrutvik Bhavsar, Franca Rossi, Menico Rizzi, Brian T Chait, Riccardo Miggiano, David Jeruzalmi.

Replicative helicases are assembled on chromosomes by helicase loaders before the initiation of DNA replication. Here, we investigate the mechanisms employed by the bacterial Vibrio cholerae (Vc) DnaB replicative helicase and the DciA helicase loader. Structural analysis of the ATPγS form of the VcDnaB-ssDNA complex reveals a configuration distinct from that observed with GDP•AlF4. With ATPγS, the amino-terminal domain (NTD) tier, previously found as an open spiral in the GDP•AlF4 complex, adopts a closed planar arrangement. Furthermore, the DnaB subunit at the top of the carboxy-terminal domain (CTD) spiral is displaced by approximately 25 Å between the two forms. We suggest that remodeling the NTD layer between closed planar and open spiral configurations, along with the migration of two distinct CTDs to the top of the DnaB spiral, repeated three times, mediates hand-over-hand translocation. Biochemical analysis indicates that VcDciA utilizes its Lasso domain to interact with DnaB near its Docking-Helix Linker-Helix interface. Up to three copies of VcDciA bind to VcDnaB, suppressing its ATPase activity during loading onto physiological DNA substrates. Our data suggest that DciA loads DnaB onto DNA using the ring-opening mechanism.

DOI: https://doi.org/10.1093/nar/gkaf521