# Mechanistic coupling of enzymatic activities at the replisome

**Authors:** Malisha U. Welikala, Lauren J. Butterworth, Rashini Y. Beragama Arachchi, Michael A. Trakselis

PMC · DOI: 10.1016/j.jbc.2025.110761 · The Journal of Biological Chemistry · 2025-09-24

## TL;DR

This paper reviews how DNA replication enzymes work together across different organisms, highlighting conserved mechanisms and their implications for replication-related diseases.

## Contribution

The paper provides a comparative analysis of replisome coupling mechanisms across diverse systems, emphasizing conserved and adaptive strategies.

## Key findings

- Replisome systems across phage, E. coli, and eukaryotes share conserved coordination principles through helicase interactions.
- Differences in replisome complexity reveal both universal and divergent strategies for replication regulation.
- Stalled replication forks and single-strand gaps are linked to conserved regulatory responses across species.

## Abstract

DNA replication is a vital process requiring the synergistic coordination of enzymatic activities that include unwinding, priming, and synthesis. The helicase serves as the central hub of the replisome and maintains interactions with the enzymes involved in priming and synthesis, which can alter respective structural conformations to control kinetics. This review compares how evolutionarily diverse model systems from phage, Escherichia coli, and eukaryotes mechanistically couple these functions to maintain replication stability amid genomic challenges. Despite vast differences in complexity, all systems exhibit conserved principles of coordination through helicase–primase and helicase–polymerase interactions, facilitated by direct binding, intermediary proteins, or conformational constraints. We explore the structural and functional dynamics of replisome architecture, highlighting how core enzymes and accessory proteins collaborate to stabilize and regulate these complexes. Differences in replisome complexity, from the streamlined T7 to more intricate eukaryotic systems, underscore conserved and adaptive strategies for replication regulation. Consequences of replisome blocks leading to stalled forks or decoupled unwinding and synthesis, giving rise to single-strand gaps, are discussed in the context of conserved regulatory responses. Together, we provide insight into universal and divergent replisomal coupling mechanisms, offering a foundation for understanding replication-associated diseases and informing on novel therapeutic approaches.

## Linked entities

- **Proteins:** HFM1 (helicase for meiosis 1), primase (hypothetical protein), ERVK-9 (endogenous retrovirus group K member 9)
- **Species:** Escherichia coli (taxon 562)

## Full-text entities

- **Genes:** MCM2 (MCM DNA helicase complex subunit MCM2) [NCBI Gene 852258], DPB4 (DNA polymerase epsilon noncatalytic subunit) [NCBI Gene 851699], DPB2 (DNA polymerase epsilon noncatalytic subunit) [NCBI Gene 856305], RAD1 (ssDNA endodeoxyribonuclease RAD1) [NCBI Gene 856085] {aka LPB9, RAD12}, CHK1 (serine/threonine protein kinase CHK1) [NCBI Gene 852577], PSF3 (DNA replication protein PSF3) [NCBI Gene 854019], PRI2 (DNA primase subunit PRI2) [NCBI Gene 853821], RAD9 (chromatin-binding protein RAD9) [NCBI Gene 851803], HCA4 (RNA-dependent ATPase HCA4) [NCBI Gene 853419] {aka DBP4, ECM24}, DBP3 (RNA-dependent ATPase DBP3) [NCBI Gene 852802], SLD5 (DNA replication protein SLD5) [NCBI Gene 852100] {aka CDC105}, DBP2 (DEAD-box ATP-dependent RNA helicase DBP2) [NCBI Gene 855611], TOF1 (Tof1p) [NCBI Gene 855448], CSM3 (Csm3p) [NCBI Gene 855067], MCM10 (Mcm10p) [NCBI Gene 854656] {aka DNA43}, POL12 (DNA-directed DNA polymerase alpha subunit POL12) [NCBI Gene 852245], SSB [NCBI Gene 20466802], CTF4 (chromatin-binding protein CTF4) [NCBI Gene 856254] {aka CHL15, POB1}, DPB3 (DNA polymerase epsilon noncatalytic subunit) [NCBI Gene 852580], RRM3 (DNA helicase) [NCBI Gene 856426] {aka RTT104}, PSF2 (DNA replication protein PSF2) [NCBI Gene 853373] {aka CDC102}, MCM3 (MCM DNA helicase complex subunit MCM3) [NCBI Gene 856680], Helicase [NCBI Gene 1261048], POL3 (DNA-directed DNA polymerase delta POL3) [NCBI Gene 851456] {aka CDC2, HPR6, TEX1}, PSF1 (DNA replication protein PSF1) [NCBI Gene 851576] {aka CDC101}, GEF1 (Gef1p) [NCBI Gene 853497] {aka CLC}, PRI1 (DNA primase subunit PRI1) [NCBI Gene 854825], POL31 (DNA-directed DNA polymerase delta subunit POL31) [NCBI Gene 853462] {aka HUS2, HYS2, SDP5}, POL32 (DNA polymerase delta subunit POL32) [NCBI Gene 853500] {aka REV5}, FOB1 (replication fork barrier binding protein FOB1) [NCBI Gene 851688] {aka HRM1}, POL2 (DNA polymerase epsilon catalytic subunit) [NCBI Gene 855459] {aka DUN2}, Rep [NCBI Gene 5548066], HIS2 (histidinol-phosphatase) [NCBI Gene 850581], RAD53 (serine/threonine/tyrosine protein kinase RAD53) [NCBI Gene 855950] {aka LSD1, MEC2, SPK1}, MRC1 (chromatin-modulating protein MRC1) [NCBI Gene 850297] {aka YCL060C}, PIF1 (DNA helicase PIF1) [NCBI Gene 854941] {aka TST1}, POL1 (DNA-directed DNA polymerase alpha catalytic subunit POL1) [NCBI Gene 855621] {aka CDC17, CRT5, HPR3}, CDC45 (DNA replication initiation factor CDC45) [NCBI Gene 850793] {aka SLD4}, MCM5 (MCM DNA helicase complex subunit MCM5) [NCBI Gene 850980] {aka BOB1, CDC46}
- **Diseases:** intrauterine growth retardation (MESH:D005317), DPCs (MESH:D011488), neurological diseases (MESH:D020271), cancer (MESH:D009369), TLS (MESH:C536766), NK cell deficiency (MESH:D054066), chronic neutropenia (MESH:C535815)
- **Chemicals:** CMG (-), dTTP (MESH:C024157), nucleotides (MESH:D009711), aldehydes (MESH:D000447), ATP (MESH:D000255), cyclobutane (MESH:D003503)
- **Species:** Escherichia phage T7 (no rank) [taxon 10760], Xenopus laevis (African clawed frog, species) [taxon 8355], Tequatrovirus T4 (species) [taxon 10665], Homo sapiens (human, species) [taxon 9606], Aspergillus nidulans (species) [taxon 162425], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Schizosaccharomyces pombe (fission yeast, species) [taxon 4896], Escherichia coli (E. coli, species) [taxon 562]
- **Cell lines:** T7 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_4E63)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12593628/full.md

## References

254 references — full list in the complete paper: https://tomesphere.com/paper/PMC12593628/full.md

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Source: https://tomesphere.com/paper/PMC12593628