Interplay between cohesin and TORC1 links chromosome segregation and gene expression to environmental changes

Reviewer #1 (Public review):

Summary:

In this study, Besson et al. investigate how environmental nutrient signals regulate chromosome biology through the TORC1 signaling pathway in Schizosaccharomyces pombe. Specifically, the authors explore the impact of TORC1 on cohesin function - a protein complex essential for chromosome segregation and transcriptional regulation. Through a combination of genetic screens, biochemical analysis, phospho-proteomics, and transcriptional profiling, they uncover a functional and physical interaction between TORC1 and cohesin. The data suggest that reduced TORC1 activity enhances cohesin binding to chromosomes and improves chromosome segregation, with implications for stress-responsive gene expression, especially in subtelomeric regions.

Strengths:

This work presents a compelling link between nutrient sensing and chromosome regulation. The major strength of the study lies in its comprehensive and multi-disciplinary approach. The authors integrate genetic suppression screens, live-cell imaging, chromatin immunoprecipitation, co-immunoprecipitation, and mass spectrometry to uncover the functional connection between TORC1 signaling and cohesin. The use of phospho-mutant alleles of cohesin subunits and their loader provides mechanistic insight into the regulatory role of phosphorylation. The addition of transcriptomic analysis further strengthens the biological relevance of the findings and places them in a broader physiological context. Altogether, the dataset convincingly supports the authors' main conclusions and opens up new avenues of investigation.

Weaknesses:

While the study is strong overall, a few limitations are worth noting. The consistency of cohesin phosphorylation changes under different TORC1-inhibiting conditions (e.g., genetic mutants vs. rapamycin treatment) is unclear and could benefit from further clarification. The phosphorylation sites identified on cohesin subunits do not match known AGC kinase consensus motifs, raising the possibility that the modifications are indirect. The study relies heavily on one TORC1 mutant allele (mip1-R401G), and additional alleles could strengthen the generality of the findings. Furthermore, while the results suggest that nutrient availability influences cohesin function, this is not directly tested by comparing growth or cohesin dynamics under defined nutrient conditions.

Reviewer #2 (Public review):

Summary:

In this study, the authors follow up on a previous suppressor screen of a temperature-sensitive allele of mis4 (mis4-G1487D), the cohesin loading factor in S. pombe, and identify additional suppressor alleles tied to the S. pombe TORC1 complex. Their analysis suggests that these suppressor mutations attenuate TORC1 activity, while enhanced TORC1 activity is deleterious in this context. Suppression of TORC1 activity also ameliorates chromosome segregation and spindle defects observed in the mis4-G1487D strain, although some more subtle effects are not reconstituted. The authors provide evidence that this genetic suppression is also tied to the reconstitution of cohesin loading. Moreover, disrupting TORC1 also enhances Mis4/cohesin association with chromatin (likely reflecting enhanced loading) in WT cells, while rapamycin treatment can enhance the robustness of chromosome transmission. These effects likely arise directly through TORC1 or its downstream effector kinases, as TORC1 co-purifies with Mis4 and Rad21; these factors are also phosphorylated in a TORC1-dependent fashion. Disrupting Sck2, a kinase downstream of TORC1, also suppresses the mis4-G1487D allele while simultaneous disruption of Sck1 and Sck2 enhances cohesin association with chromatin, albeit with differing effects on phosphorylation of Mis4 and Psm1/Scm1. Phosphomutants of Mis4 and Psm1 that mimic observed phosphorylation states identified by mass spectrometry that are TORC1-dependent also suppressed phenotypes observed in the mis4-G1487D background. Last, the authors provide evidence that the mis4-G1487D background and TORC1 mutant backgrounds display an overlap in the dysregulation of genes that respond to environmental conditions, particularly in genes tied to meiosis or other "stress".

Overall, the authors provide compelling evidence from genetics, biochemistry, and cell biology to support a previously unknown mechanism by which nutrient sensing regulates cohesin loading with implications for the stress response. The technical approaches are generally sound, well-controlled, and comprehensive.

Specific Points:

(1) While the authors favor the model that the enhanced cohesin loading upon diminished TORC1 activity helps cells to survive harsh environmental conditions, as starvation of S. pombe also drives commitment to meiosis, it seems as plausible that enhanced cohesin loading is related to preparing the chromosomes to mate.

(2) Related to Point 1, the lab of Sophie Martin previously published that phosphorylation of Mis4 characterizes a cluster of phosphotargets during starvation/meiotic induction (PMID: 39705284). This work should be cited, and the authors should interrogate how their observations do or do not relate to these prior observations (are these the same phosphosites?).

(3) It would be useful for the authors to combine their experimental data sets to interrogate whether there is a relationship between the regions where gene expression is altered in the mis4-G1487D strain and changes in the loading of cohesin in their ChIP experiments.

(4) Given that the genes that are affected are predominantly sub-telomeric while most genes are not affected in the mis4-G1487D strain, one possibility that the authors may wish to consider is that the regions that become dysregulated are tied to heterochromatic regions where Swi6/HP1 has been implicated in cohesin loading.

(5) It would be helpful to show individual data points from replicates in the bar graphs - it is not always clear what comprises the data sets, and superplots would be of great help.