Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic DOI Creative Commons
Frank Bürmann, Bryony Clifton,

Sophie Koekemoer

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms DNA entrapment loop extrusion. Here, we explore the loading process bacterial SMC complex MukBEF. Using cryoelectron microscopy (cryo-EM), demonstrate that ATP binding opens one MukBEF's three potential entry gates, exposing a capture site positions at open neck gate. We discover gp5.9 protein bacteriophage T7 blocks this by mimicry, thereby preventing inactivating propose comprehensive unidirectional mechanism in which is first captured complex's periphery then ingested gate, powered single cycle hydrolysis. These findings illuminate fundamental aspect how ubiquitous organizers primed can be disrupted viruses.

Language: Английский

SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo DOI Creative Commons
Zhongqing Ren, Lindsey E. Way, Xindan Wang

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 19, 2025

Genome organization is important for DNA replication, gene expression, and chromosome segregation. In bacteria, two large families of proteins, nucleoid-associated proteins (NAPs) SMC complexes, play roles in organizing the genome. NAPs are highly abundant DNA-binding that can bend, wrap, bridge, compact DNA, while complexes load onto chromosome, translocate on extrude loops. Although capable traversing entire bound by various vivo, it unclear whether translocation influenced NAPs. this study, using Bacillus subtilis as a model system, we expressed collection representative bacterial archaeal introduce distinct structures potentially pose different challenges movement. By fluorescence microscopy chromatin immunoprecipitation, observed these to genome characteristic manners. Using genome-wide conformation capture (Hi-C) assays, found complex traversed without slowing down. Our findings revealed DNA-loop-extruding activity unaffected exogenously which highlights robustness motors busy chromatin.

Language: Английский

Citations

1
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure DOI Creative Commons

Kodai Yamaura,

Naomichi Takemata,

Masashi Kariya

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 19, 2025

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

Language: Английский

Citations

0
A unified model for cohesin function in sisterchromatid cohesion and chromatin loop formation DOI Creative Commons
Frank Uhlmann

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(6), P. 1058 - 1071

Published: March 1, 2025

The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape by forming DNA loops, which it is thought achieve using an in vitro-observed loop extrusion mechanism. However, recent studies revealed that loop-extrusion-deficient retains its ability form suggesting a divergence of vitro and vivo formation. Instead extrusion, we examine whether forms loops mechanism akin cohesion establishment: sequential topological capture DNAs. We explore similarities differences between "loop capture" extrusion" model, how they compare at explaining experimental observations, future approaches can delineate their possible respective contributions. extend our DNA-DNA model for function related structural maintenance chromosomes (SMC) family members, condensin, Smc5-Smc6 complex, bacterial SMC complexes.

Language: Английский

Citations

0
Structural basis of antiphage defense by an ATPase-associated reverse transcriptase DOI Creative Commons
Jerrin Thomas George, Nathaniel Burman, Royce A. Wilkinson

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses retrotransposons. However, recent evidence suggests that RTs been conscripted by cells for diverse antiviral defense. Here we determine structures a type I-A retron, which explain how RNA, DNA, RT, HNH-nuclease four molecules an SMC-family ATPase assemble into 364 kDa complex provides phage We show phage-encoded nucleases trigger degradation retron-associated leading to disassembly retron activation HNH nuclease. The nuclease cleaves tRNA Ser , stalling protein synthesis arresting viral replication. Taken together, these data reveal paradoxical perpetuation elimination genetic parasites.

Language: Английский

Citations

0
Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery DOI Creative Commons
Matthieu Haudiquet, A. Chakravarti, Zhiying Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, evolutionary origins many antiphage remain elusive, especially for those that encode homologs Structural Maintenance Chromosomes (SMC) superfamily, which are essential chromosome maintenance DNA repair across domains life. Here, we elucidate structural basis emergence Lamassu, bacterial system family featuring diverse effectors but core conserved SMC-like sensor. Using cryo-EM, determined structures Vibrio cholerae Lamassu complex in both apo- dsDNA-bound states, revealing unexpected stoichiometry topological architectures. We further demonstrate how specifically senses dsDNA vitro replication vivo , thereby triggering formation LmuA tetramers activate Cap4 nuclease domain. Our findings reveal evolved via exaptation Rad50-Mre11 to form compact, modular sensor viral replication, exemplifying cellular machinery can be co-opted novel functions.

Language: Английский

Citations

0
Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic DOI Creative Commons
Frank Bürmann, Bryony Clifton,

Sophie Koekemoer

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Ring-like structural maintenance of chromosome (SMC) complexes are crucial for genome organization and operate through mechanisms DNA entrapment loop extrusion. Here, we explore the loading process bacterial SMC complex MukBEF. Using cryoelectron microscopy (cryo-EM), demonstrate that ATP binding opens one MukBEF's three potential entry gates, exposing a capture site positions at open neck gate. We discover gp5.9 protein bacteriophage T7 blocks this by mimicry, thereby preventing inactivating propose comprehensive unidirectional mechanism in which is first captured complex's periphery then ingested gate, powered single cycle hydrolysis. These findings illuminate fundamental aspect how ubiquitous organizers primed can be disrupted viruses.

Language: Английский

Citations

0