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Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure

Author

Listed:
  • Kodai Yamaura

    (Kyoto University)

  • Naomichi Takemata

    (Kyoto University)

  • Masashi Kariya

    (Kyoto University)

  • Ayami Osaka

    (Kyoto University)

  • Sonoko Ishino

    (Kyushu University
    Nagahama Institute of Bio-Science and Technology)

  • Masataka Yamauchi

    (Kyoto University)

  • Tomonori Tamura

    (Kyoto University)

  • Itaru Hamachi

    (Kyoto University)

  • Shoji Takada

    (Kyoto University)

  • Yoshizumi Ishino

    (Kyushu University
    Nagahama Institute of Bio-Science and Technology
    Institute of Science Tokyo)

  • Haruyuki Atomi

    (Kyoto University)

Abstract

In eukaryotes, structural maintenance of chromosomes (SMC) complexes form topologically associating domains (TADs) by extruding DNA loops and being stalled by roadblock proteins. It remains unclear whether a similar mechanism of domain formation exists in prokaryotes. Using high-resolution chromosome conformation capture sequencing, we show that an archaeal homolog of the bacterial Smc-ScpAB complex organizes the genome of Thermococcus kodakarensis into TAD-like domains. We find that TrmBL2, a nucleoid-associated protein that forms a stiff nucleoprotein filament, stalls the T. kodakarensis SMC complex and establishes a boundary at the site-specific recombination site dif. TrmBL2 stalls the SMC complex at tens of additional non-boundary loci with lower efficiency. Intriguingly, the stalling efficiency is correlated with structural properties of underlying DNA sequences. Our study illuminates a eukaryotic-like mechanism of domain formation in archaea and a role of intrinsic DNA structure in large-scale genome organization.

Suggested Citation

  • Kodai Yamaura & Naomichi Takemata & Masashi Kariya & Ayami Osaka & Sonoko Ishino & Masataka Yamauchi & Tomonori Tamura & Itaru Hamachi & Shoji Takada & Yoshizumi Ishino & Haruyuki Atomi, 2025. "Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56197-y
    DOI: 10.1038/s41467-025-56197-y
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