Link to our unpublished work on bioRxiv

Link to all publications

bioRxiv preprints

The largest SWI/SNF polyglutamine domain is a pH sensor Gutiérrez, J.I., Brittingham, G.P., Wang, X., Fenyö, D., Holt, L.J. biRxiv (2017) doi: https://doi.org/10.1101/165043

Latrodectus hesperus.jpg

Why is there a terrifying image of a spider here? Don’t worry, there are no terrifying spiders in the lab. We did scare reviewers though.

Polyglutamines are known to form aggregates in pathogenic contexts, such as Huntington disease. However, little is known about their normal biological role. We found that the polyglutamine domain senses transient cytosolic acidification under stress conditions and helps reprogram transcription. This reveals a new important biological role for polyglutamine domains beyond the disease context.

Selected papers

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding Delarue M., Brittingham G.P., Pfeffer S., Surovtsev I.V., Pinglay S., Kennedy K.J., Schaffer M., Gutierrez J.I., Sang D., Poterewicz G., Chung J.K., Plitzko J.M., Groves J.T., Jacobs-Wagner C., Engel B.D., Holt L.J. Cell. 2018 Jul 12

cell-mtorc1-graphical-abstract.jpg

This paper shows that the central growth regulator mTORC1 determines the physical properties of the cytoplasm! By modulating the concentration of ribosomes through production and autophagy, the rates of diffusion of everything in the cell that is > 20 nm diameter can be varied 2-fold in yeast and 20% in humans. Therefore, all of the second-order rate constants for any reasonably-sized complex in the cell is not constant. Also, phase separation is substantially regulated by this crowding regulation.

 

SCWISh network is essential for survival under mechanical pressure Delarue M., Poterewicz G., Hoxha O., Choi J., Yoo W., Kayser J., Holt L.J.*, Hallatschek O.* PNAS 2017 Dec 19

InstantPressure.jpg

We know quite a bit about how cells sense tensile stresses, but almost nothing about how cells detect and respond to mechanical compressive stress (pressure). All of the cells in our body are under pressure. We should probably figure this out. This paper describes the SCWISh pathway, required for cells to survive when growing under pressure! At the top of the pathway is a mucin. Mucins are frequently misregulated in cancer. We think these sensors will play an important role in the adaptation of cancer to new mechanical conditions.

 

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity Howard, C., Hanson-Smith, V., Kennedy, K.J., Miller, C.J., Lou, H.J., Johnson, A.D., Turk, B., and Holt, L.J. Elife 2014 3.

STRIKING-IMAGE-1.png

Amazingly, we can reconstruct and resurrect kinases from >2 billion years ago and determine their specificity! The deep ancestors of Cdk1, MAP kinases and Ime2 reveal that the gatekeeper residue helps determine specificity. This paper also suggests that kinase networks can tolerate new information, thus providing a pathway for dramatic rewiring of the cell's circuitry.

 

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution. Holt, L.J., Tuch, B., Villen, J., Johnson, A., Gygi, S., and Morgan, D. Science 2009

Cdk1-evolution.jpg

We combined the "Shokat" analog-sensitive kinase approach with SILAC quantitative mass spectrometry (with the Gygi lab) to discover >300 Cdk1 substrates in S. cerevisiae. Evolutionary analysis revealed that these sites, while often conserved for >1 billion years (bottom), are very rarely conserved in terms of their precise position (top). This work suggests that phosphorylation networks are quite evolvable. Biological information systems can change readily to adapt to new challenges.

 

Positive feedback sharpens the anaphase switch. Holt, L.J., Krutchinsky, A.N., and Morgan, D.O. Nature 2008

Anaphase.jpg

Positive feedback can generate switch-like behaviors where systems abruptly and irreversibly transition from one state to another (bistability). We found a positive feedback look involving Cdk1, Cdc14, Securin, Separase and the Anaphase Promoting Complex (some of the tastiest spices in the soup of regulators that is the cell cycle). This feedback loop ensures synchronous chromosome segregation at anaphase onset and improves the fidelity of cell division.