Biology subjects

Koshland, D.

Publications and source records attributed to Koshland, D..

9 recordsLinked to original sources

bioRxiv2026

Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange

The protein complex cohesin plays critical roles in genomic stability by tethering together sister chromatids at their pericentric regions and along their arms from S phase until anaphase. Cohesin-mediated pericentric cohesion prevents aneuploidy by ensuring bipolar attachment of sister kinetochores. Arm cohesion prevents loss of heterozygosity by biasing DNA repair via recombination between sister chromatids rather than between homologs. Here, we investigate in yeast whether cohesin also enhances genomic stability by suppressing unequal sister chromatid exchange (USCE) between repetitive sequences. In wild-type cells, the USCE rate between repeats 4kb apart (proximal) was 15X higher than repeats 68kb apart (distal). The USCE between distal repeats but not proximal repeats increased 4 to 7-fold in mutants with altered cohesin subunits or auxiliary factors. The level of increased distal USCE corresponded with reduced arm cohesion, reduced density of cohesion arm sites, and higher sister loci mobility. Our results suggest that high density of arm cohesion sites confines repair of DNA damage to local sequences. When the density of cohesion sites decreases, sister chromatid sequences are less confined, thereby enhancing distal repeat interactions and USCE. Another set of mutations disrupted both DNA replication and cohesin loading at the replication fork during S phase. Remarkably, distal USCE in these mutants increased approximately 100-fold and was 6-fold more likely than proximal USCE. This preferential hyperdistal USCE can be explained by an aberrant sister-chromatid structure that is normally prevented by proper coupling of cohesin function and replication.

genetics↗

bioRxiv2025

Cohesin Acetylation and ATPase Activity Control Cohesion and Loop Architecture through Distinct Mechanisms

Cohesin is a conserved protein complex that mediates sister chromatid cohesion, chromosome condensation, gene regulation, and DNA repair. These processes rely on cohesins ability to tether sister chromatids and form chromatin loops, which depend on cohesins ATPase activity and Eco1-mediated acetylation of two lysine residues (K112 and K113 in budding yeast) in its Smc3 subunit. How cohesins ATPase activity and acetylation integrate to control cohesin functions remains poorly understood. Here, we analyzed chromatin architecture in yeast mutants with altered cohesin acetylation and/or ATPase activity. We find that acetylation of either K112 or K113 is sufficient to produce a wild-type chromosome structure with loops positioned at cohesin-associated regions (CARs), whereas loss of acetylation at both residues abolishes positioned loops, indicating that acetylation at either lysine alone can maintain wild-type chromatin architecture. We further show that a cohesin acetylation mutant, despite being defective in sister-chromatid tethering and thus failing to establish cohesion, still forms wild-type-like loops, while cohesion-competent mutants lack positioned loops. These results suggest that the activities required for cohesion and loop formation are mechanistically separable, arguing against passive loop capture. Moreover, a mutant with reduced ATPase activity showed a loop profile similar to wild type, indicating that cohesin with lower ATPase activity can still form wild-type chromatin architecture. By contrast, hyper-ATPase mutants accumulate positioned loops, suggesting that increasing ATPase activity can enhance loop processivity. Together, our findings support a multilayered regulatory model in which acetylation fine-tunes ATPase output and cohesin functions to shape genome architecture.

genetics↗

bioRxiv2022

A model for Scc2p Stimulation of Cohesin's ATPase and its Inhibition by Acetylation of Smc3p

The evolutionarily conserved cohesin complex mediates sister chromatid cohesion and facilitates mitotic chromosome condensation, DNA repair, and transcription regulation. These biological functions require cohesins two ATPases, formed by the Smc1p and Smc3p subunits. Cohesins ATPase activity is stimulated by the Scc2p auxiliary factor. This stimulation is inhibited by Eco1p acetylation of Smc3p at an interface with Scc2p. It was unclear how cohesins ATPase activity is stimulated by Scc2p, or how acetylation inhibits Scc2p, given that the acetylation site is distal to cohesins ATPase active sites. Here, we identify mutations in budding yeast that suppressed the in vivo defects caused by Smc3p acetyl-mimic and acetyl-defective mutations. We provide compelling evidence that Scc2p activation of cohesin ATPase depends upon an interface between Scc2p and a region of Smc1p proximal to cohesins Smc3p ATPase active site. Furthermore, substitutions at this interface increase or decrease ATPase activity to overcome ATPase modulation by acetyl-mimic and - null mutations. Using these observations and a cryo-EM structure, we propose a model for regulating cohesin ATPase activity. We suggest that Scc2p binding to Smc1p causes a shift in adjacent Smc1p residues and ATP, stimulating the Smc3p ATPase. This stimulatory shift is inhibited through acetylation of the distal Scc2p-Smc3 interface.

genetics↗

bioRxiv2020

Cohesin in space and time: architecture and oligomerization in vivo.

Cohesin helps mediate sister chromatid cohesion, chromosome condensation, DNA repair and transcription regulation. Cohesin can tether two regions of DNA and can also extrude DNA loops. We interrogated cohesin architecture, oligomerization state and function of cohesin oligomers in vivo through proximity-dependent labeling of cohesin domains. Our results suggest that the hinge and head domains of cohesin both bind DNA, and that cohesin coiled coils bend, bringing the head and hinge together to form a butterfly conformation. Our data also suggest that cohesin efficiently oligomerizes on and off DNA. The levels of oligomers and their distribution on chromosomes are cell cycle regulated. Cohesin oligomerization is blocked by mutations in distinct domains of Smc3p and Mcd1p, or depletion of Pds5p. This unusual subset of mutations specifically blocks the maintenance of cohesion and condensation, suggesting that cohesin oligomerization plays a critical role in these biological functions.

genetics↗

bioRxiv2019

THE SPATIAL REGULATION OF CONDENSIN ACTIVITY IN CHROMOSOME CONDENSATION

Condensin mediates chromosome condensation, which is essential for proper chromosome segregation during mitosis. Prior to anaphase of budding yeast, the ribosomal DNA (RDN) condenses to a thin loop that is distinct from the rest of the chromosomes. We provide evidence that the establishment and maintenance of this RDN condensation require the regulation of condensin by Cdc5p (polo) kinase. We show that Cdc5p is recruited to the site of condensin binding in the RDN by cohesin, a complex related to condensin. Cdc5p and cohesin prevent condensin from misfolding the RDN into an irreversibly decondensed state. From these and other observations, we propose that the spatial regulation of Cdc5p by cohesin modulates condensin activity to ensure proper RDN folding into a thin loop. This mechanism may be evolutionarily conserved, promoting the thinly condensed constrictions that occur at centromeres and RDN of mitotic chromosomes in plants and animals.

genetics↗

bioRxiv2019

Communication between distinct subunit interfaces of the cohesin complex promotes its topological entrapment of DNA.

Cohesin mediates higher-order chromosome structure. Its biological activities require topological entrapment of DNA within a lumen(s) formed by cohesin subunits. The reversible dissociation of cohesins Smc3p and Mcd1p subunits are postulated to form a regulated gate that allows DNA entry and exit into the lumen. We assessed gate-independent functions of this interface in yeast using a fusion protein that joins Smc3p to Mcd1p. We show that in vivo all the regulators of cohesin promote DNA binding of cohesion by mechanisms independent of opening this gate. Furthermore, we show that this interface has a gate-independent activity essential for cohesin to bind chromosomes. We propose this interface regulates DNA entrapment by controlling the opening and closing of one or more distal interfaces formed by cohesin subunits, likely by inducing a conformation change in cohesin. Furthermore, cohesin regulators modulate the interface to control both DNA entrapment and cohesin functions after DNA binding.

genetics↗

bioRxiv2017

Synergism between a simple sugar and a small intrinsically disordered protein mitigate the lethal stresses of severe water loss

Anhydrobiotes are rare microbes, plants and animals that tolerate severe water loss. Understanding the molecular basis for their desiccation tolerance may provide novel insights into stress biology and critical tools for engineering drought-tolerant crops. Using the anhydrobiote, budding yeast, we show that trehalose and Hsp12, a small intrinsically disordered protein (sIDP) of the hydrophilin family, synergize to mitigate completely the inviability caused by the lethal stresses of desiccation. We show that these two molecules help to stabilize the activity and prevent aggregation of model proteins both in vivo and in vitro. We also identify a novel role for Hsp12 as a membrane remodeler, a protective feature not shared by another yeast hydrophilin, suggesting that sIDPs have distinct biological functions.

cell biology↗

bioRxiv2017

A role for the Smc3 hinge domain in the maintenance of sister chromatid cohesion

Cohesin is a conserved protein complex required for sister chromatid cohesion, chromosome condensation, DNA damage repair, and regulation of transcription. Although cohesin functions to tether DNA duplexes, the contribution of its individual domains to this activity remains poorly understood. We interrogated the Smc3p subunit of cohesin by random insertion mutagenesis. Analysis of a mutant in the Smc3p hinge revealed an unexpected role for this domain in cohesion maintenance and condensation. Further investigation revealed that the Smc3p hinge functions at a step following cohesins stable binding to chromosomes and independently of Smc3ps regulation by the Eco1p acetyltransferase. Hinge mutant phenotypes resemble loss of Pds5p, which binds opposite the hinge near Smc3ps head domain. We propose that a specific conformation of the Smc3p hinge and Pds5p cooperate to promote cohesion maintenance and condensation.

cell biology↗

bioRxiv2017

Budding yeast Wpl1p regulates cohesin functions in cohesion, condensation and DNA repair by a common mechanism

Cohesin tethers DNA to mediate sister chromatid cohesion, chromosome condensation, and DNA repair. How the cell regulates cohesin to perform these distinct functions remains to be elucidated. One cohesin regulator, Wpl1p, was characterized in the budding yeast, Saccharomyces cerevisiae, as a promoter of cohesion and as an inhibitor of condensation. Here we provide evidence that Wpl1p has an additional function in promoting the timely repair of DNA damage induced during S-phase. In addition to these biological functions, Wpl1p has been implicated as an inhibitor of cohesins ability to stably bind DNA by modulating the interface between two subunits (Mcd1p and Smc3p) of the core cohesin complex. We show that Wpl1p likely modulates this interface to regulate all cohesins biological functions. Furthermore, we show that Wpl1p regulates cohesion and condensation through the formation of a functional complex with another cohesin-associated factor, Pds5p. In contrast, Wpl1p regulates DNA repair independently of its interaction with Pds5p. Together these results suggest that Wpl1p regulates distinct biological functions of cohesin by Pds5p-dependent and - independent modulation of the Smc3p-Mcd1p interface.

genetics↗