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

Kodai Yamaura, Naomichi Takemata (), Masashi Kariya, Ayami Osaka, Sonoko Ishino, Masataka Yamauchi, Tomonori Tamura, Itaru Hamachi, Shoji Takada, Yoshizumi Ishino and Haruyuki Atomi ()
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Kodai Yamaura: Kyoto University
Naomichi Takemata: Kyoto University
Masashi Kariya: Kyoto University
Ayami Osaka: Kyoto University
Sonoko Ishino: Kyushu University
Masataka Yamauchi: Kyoto University
Tomonori Tamura: Kyoto University
Itaru Hamachi: Kyoto University
Shoji Takada: Kyoto University
Yoshizumi Ishino: Kyushu University
Haruyuki Atomi: Kyoto University

Nature Communications, 2025, vol. 16, issue 1, 1-21

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-56197-y

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