Jeremy Thorner

Jeremy Thorner

Distinguished Professor Emeritus of Biochemistry, Biophysics and Structural Biology*
*And William V. Power Chair in Biology (1991-2011), And Affiliate, Division of Cell Biology, Development & Physiology

Env Full Directory Information

Research Interests

Transmembrane and intracellular signal transduction mechanisms are the focus of our group, especially understanding how extracellular stimuli control cell growth and division, cell morphology, and gene expression at the biochemical level.

Current Projects

Although I retired from active faculty service (as of 1 July 2020), I continued to teach full-time (one last time) in academic year 2020-21.  However, research operations in my laboratory closed down, permanently, on 30 June 2021.  During the past several years, most of our research efforts were focused on the following projects.  See also citations to published work below.

Protein kinases that control plasma membrane lipid homeostasis. We have shown that Ypk1, a member of the AGC class of protein kinases conserved from yeast to humans, is the essential target of and activated via phosphorylation by the plasma membrane-associated TORC2 complex. Ypk1, in turn, regulates (via its phosphorylation of multiple substrates) maintenance of sphingolipid and glycerolipid homeostasis and bilayer lipid organization in the plasma membrane. We have recently shown that this same pathway modulates the content of integral membrane proteins and, in collaborative studies, that it is also involved in maintenance of the sterol composition of the plasma membrane. For these reasons, this pathway and the mechanisms by which TORC2 and Ypk1 are regulated are under continuing intensive study.  In this regard, we have recently shown that efficient activation of Ypk1 by TORC2 requires stimulation of TORC2 by the GTP-bound state of a Rab5 GTPase (Vps21/Ypt51) and that, in turn, Rab5-dependent endocytosis may be a mechanism to down-regulate TORC2 signaling after it has been activated.

Previous research projects that, in some cases, are also on-going in collaboration with former graduate students or former postdoctoral fellows, or with collaborators on this campus or elsewhere, include:

The roles of septins and septin-associated protein kinases in cell morphogenesis and cell cycle control. The Wee1 class of protein-tyrosine kinase has an important role in cell cycle control. We investigated control mechanisms that regulate the activity, localization, and stability of Wee1, especially the bud neck-localized protein kinase Hsl1 and its more distant paralogs (Gin4 and Kcc4), in particular their recruitment to septin filaments, which assemble at the presumptive site of cell division. We have shown that septin filaments are assembled from hetero-octameric complexes containing two each of four different septin subunits.  We also studied the roles of other classes of protein kinases (Cla4) and additional post-translational modifications (SUMOylation) in septin complex assembly, formation of different septin-based supramolecular ensembles, disassembly of septin-containing structures, and the function of septin organization in the events required for cell division and membrane septation during cytokinesis. Our past studies on septin ultrastructure were, in many cases, conducted in close collaboration with our colleague Prof. Eva Nogales in our Division (BBS) of MCB.

Structural analysis of a peptide hormone receptor. To understand the molecular biology of peptide hormone action, we studied response of budding yeast (Saccharomyces cerevisiae) to its peptide mating pheromones (a-factor and α-factor). The pheromone receptors have seven hydrophobic segments and are coupled to a heterotrimeric G protein. Receptors of this type are ubiquitous and transduce binding of a wide variety of extracellular ligands (peptide hormones, neurotransmitters and other bioactive compounds) into a physiological signal. Attempts to determine the three-dimensional structure of the purified α-factor receptor by NMR and X-ray crystallography are still underway in collaborative studies with a group in Switzerland. We were also interested in proteins involved in adaptation and recovery after the pheromone-induced signal, especially:  structure and function of Sst2, the prototype RGS (Regulator of G-protein Signaling) protein; α-arrestins involved in selective ubiquitinylation and endocytosis of integral membrane proteins, including the pheromone receptors; and, various classes of phosphotyrosine-directed, phosphoserine- / phosphothreonine-directed, and dual-specificity phosphoprotein phosphatases that dephosphorylate activated MAPKs.

Molecular genetics and biochemistry of MAPK cascades. Activation of the pheromone receptor-coupled G protein initiates a four-tiered cascade of protein kinases, ultimately resulting in stimulation of a messenger-activated protein kinase or MAPK (Fus3) that translocates into the nucleus. A different developmental pathway (invasive or filamentous growth) triggered by nutrient limitation stimulates another MAPK (Kss1). Subjecting cells to hyperosmotic conditions activates yet another MAPK (Hog1). Thus, MAPK cascades are universally employed in eukaryotic cells for mounting an appropriate response to an extracellular stimulus and, like yeast, every eukaryotic cell contains multiple MAPK pathways. We investigate intensively the mechanisms that impose specificity and fidelity at each tier in these signaling networks. We showed that one device used by the cell for discrimination between parallel MAPK pathways is a specific docking interaction between a MAPK and the N-terminus of its cognate upstream protein kinase (MEK). We also showed that the scaffold protein Ste5 helps ensure signaling fidelity in pheromone response by binding the appropriate MAPK (Fus3), MEK (Ste7), and upstream activating kinase or MEKK (Ste11) and by shuttling from the nucleus to the plasma membrane, thereby delivering the MAPK module to its most proximal activator— a fourth plasma membrane-associated protein kinase (Ste20). A different scaffold protein, Ste50, is required for signal propagation in the invasive growth and hyperosmotic stress response pathways was also studied. The roles of other factors that prevent inappropriate MAPK activation in response to a given stimulus were investigated using genetic and biochemical methods.

Molecular biology of phosphoinositide-dependent signaling.  We showed that phosphatidylinositol 4-phosphate generated by a particular phosphatidylinositol 4-kinase isoform (Pik1) has a specific role in the Golgi body-to-plasma membrane stage of the secretory pathway. This enzyme also has an essential role in supplying the PtdIns(4)P that is converted to PtdIns(4,5)P2 in the nucleus, where it is hydrolyzed by a specific phospholipase C to generate inositol polyphosphates that regulate transcription, chromatin remodeling and mRNA export. We found that the phosphatidylinositol 4-kinase is also regulated by a small calcium-binding protein whose ortholog in animal cells (frequenin or neuronal calcium sensor-1) is found mainly in neuronal and neuroendocrine cells.  In other work, we explored the roles of phosphoinositides and other lipids in cell polarization, cell division and cell signaling.

Novel mechanisms for translocation across membranes. We discovered that export of the a-factor pheromone requires an integral plasma membrane protein that is a dedicated ATP-dependent transporter, rather than the classical secretory pathway. The mechanism of transmembrane translocation of pheromone by the transporter (Ste6) was examined. The functions of other members of the same transporter class, namely ABC transporters, were also studied.  Conversely, inward translocation of certain lipids from the outer to the inner leaflet of the plasma membrane is catalyzed by members of the class 4 P-type ATPase family, dubbed "flippases," which we also investigated.

Selected Publications

Bardwell L, Thorner J (2023) Mitogen-activated protein kinase (MAPK) cascades—  a yeast perspective. In The Enzymes (Kaguni L, Ed.), Vol. 54, in press.

Emmerstorfer-Augustin A, Thorner J (2023) Regulation of TORC2 function and localization in yeast.  Annu. Rev. Cell Dev. Biol. 39: 363-389.

Thorner J (2022) TOR Complex 2 is a master regulator of plasma membrane homeostasis. Biochem. J. 479: 1917-1940.

Patterson JC, Goupil LS, Thorner J (2021) Cdc42-specific GTPase-activating protein Rga1 squelches crosstalk between the high-osmolarity glycerol (HOG) and mating pheromone response MAPK pathways. Biomolecules 11: 1530.1-1530.26.

Galez HA, Roelants FM, Palm SM, Reynaud KK, Ingolia NT, Thorner J (2021) Phosphorylation of mRNA-binding proteins Puf1 and Puf2 by TORC2-activated protein kinase Ypk1 alleviates their repressive effects. Membranes (Basel) 11: 500.1-500.23. 

Takagi J, Cho C, Duvalyan A, Yan Y, Halloran M, Hanson-Smith V, Thorner J, Finnigan GC (2021) Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1. G3 (Bethesda) 11: jkaa006.

Topolska M, Roelants FM, Si EP, Thorner J (2020) TORC2-dependent Ypk1-mediated phosphorylation of Lam2/Ltc4 disrupts its association with the beta-propeller protein Laf1 at endoplasmic reticulum-plasma membrane contact sites in the yeast Saccharomyces cerevisiae. Biomolecules 10: 1598.1-1598.23.

Ablasser A, Thorner J (2020) Network news: reporting from the frontlines of cell signaling (editorial overview). Curr. Opin. Cell Biol. 63: iii-v.    

McMurray MA, Thorner J (2019) Turning it inside out: the organization of human septin hetero-oligomers. Cytoskeleton (Hoboken) 76: 449-456.

Locke MN, Thorner J (2019) Regulation of TORC2 function and localization by Rab5 GTPases in Saccharomyces cerevisiae. Cell Cycle 18: 1084-1094.

Martinez Marshall MN, Emmerstorfer-Augustin A, Leskoske KL, Zhang LH, Li B, Thorner J (2019) Analysis of the roles of phosphatidylinositol-4,5- bisphosphate and individual subunits in assembly, localization and function of Saccharomyces cerevisiae Target of Rapamycin Complex 2. Mol. Biol. Cell 30: 1555-1574.

Locke MN, Thorner J (2019) Rab5 GTPases are required for optimal TORC2 function. J. Cell Biol. 218: 961-976.

Perez AM, Thorner J (2019) Septin-associated proteins Aim44 and Nis1 traffic between the bud neck and the nucleus in the yeast Saccharomyces cerevisiae. Cytoskeleton (Hoboken) 76: 15-32.

Leskoske KL, Roelants FM, Emmerstorfer-Augustin A, Augustin CM, Si EP, Hill JM, Thorner J (2018) Phosphorylation by the stress-activated MAPK Slt2 down-regulates the yeast TOR complex 2. Genes Dev. 32: 1576-1590.

Emmerstorfer-Augustin A, Augustin CM, Shams S, Thorner J (2018) Tracking yeast pheromone receptor Ste2 endocytosis using fluorogen-activating protein tagging. Mol. Biol. Cell 29: 2720-2736. 

Roelants FM, Chauhan N, Muir A, Davis JC, Menon AK, Levine TP, Thorner J (2018) TOR Complex 2-regulated protein kinase Ypk1 controls sterol distribution by inhibiting StARkin domain-containing proteins located at plasma membrane-endoplasmic reticulum contact sites. Mol. Biol. Cell 29: 2128-2136.

Roelants FM, Leskoske KL, Martinez Marshall MN, Locke MN, Thorner J (2017) The TORC2-dependent signaling network in the yeast Saccharomyces cerevisiae. Biomolecules 7: E66 (41 pp).

Leskoske KL, Roelants FM, Marshall MNM, Hill JM, Thorner J (2017) The stress-sensing TORC2 complex activates yeast AGC-family protein kinase Ypk1 at multiple novel sites. Genetics 207: 179-195.

Roelants FM, Leskoske KL, Pedersen RT, Muir A, Liu JM, Finnigan GC, Thorner J (2017) TOR Complex 2-regulated protein kinase Fpk1 stimulates endocytosis via inhibition of Ark1/Prk1-related protein kinase Akl1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 37: e00627-16 (22pp).

Thorner J (2017) Cell Signaling: Principles & Mechanisms (Lim W et al.). - Book Review. Q. Rev. Biol. 92: 105-106.

Perez AM, Finnigan GC, Roelants FM, Thorner J (2016) Septin-associated protein kinases in the yeast Saccharomyces cerevisiae. Front. Cell Dev. Biol. 4: 119 (12pp).

Booth EA, Sterling SM, Dovala D, Nogales E, Thorner J (2016) Effects of Bni5 binding on septin filament organization, J. Mol. Biol. 428:  4962-4980.    

Sen A, Acosta-Sampson L, Alvaro CG, Ahn JS, Cate JHD, Thorner J (2016) Internalization of heterologous sugar transporters by endogenous alpha-arrestins in the yeast Saccharomyces cerevisiaeAppl. Environ. Microbiol. 82: 7074-7085.     

Guerreiro JF, Muir A, Ramachandran S, Thorner J, Sá-Correia I (2016) Sphingolipid biosynthesis upregulation by TOR Complex 2-Ypk1 signaling during yeast adaptive response to acetic acid stress. Biochem. J. 473: 4311–4325.   

Finnigan GC, Duvalyan A Liao EN, Sargsyan A, Thorner J (2016) Detection of protein-protein interactions at the septin collar in Saccharomyces cerevisiae using a tripartite split-GFP system. Mol. Biol. Cell 27: 2708-2725.

Finnigan GC, Sterling SM, Duvalyan A, Liao EN, Sargsyan A, Garcia G 3rd, Nogales E, Thorner J (2016) Coordinate action of distinct sequence elements localizes checkpoint kinase Hsl1 to the septin collar at the bud neck in Saccharomyces cerevisiae. Mol. Biol. Cell 27: 2213-2233.

Finnigan GC, Thorner J (2016) mCAL: a new approach for versatile multiplex action of Cas9 using one sgRNA and loci flanked by a programmed target sequence. G3 (Bethesda) 6: 2147-2156.

Booth EA, Thorner J (2016) A FRET-based method for monitoring septin polymerization and binding of septin-associated proteins. Methods Cell Biol. 136: 35-56.

Garcia G 3rd, Finnigan GC, Heasley LR, Sterling SM, Aggarwal A, Pearson CG, Nogales E, McMurray MA, Thorner J (2016) Assembly, molecular organization, and membrane-binding properties of development-specific septins. J. Cell Biol. 212: 515-529. 

Alvaro CG, Aindow A, Thorner J (2016) Differential phosphorylation provides a switch to control how α-arrestin Rod1 down-regulates mating pheromone response in Saccharomyces cerevisiae. Genetics 203: 299-317.

Alvaro CG, Thorner J (2016) Heterotrimeric G protein-coupled receptor signaling in yeast mating pheromone response. J. Biol. Chem. 291: 7788-7795.

Klionsky DJ et al...Thorner al. (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 12: 443.1-443.222.

Prosser DC, Pannunzio AE, Brodsky JL, Thorner J, Wendland B, O'Donnell AF (2015) α-Arrestins participate in cargo selection for both clathrin-independent and clathrin-mediated endocytosis. J. Cell Sci. 128: 4220-4234. 

Booth EA, Vane EW, Dovala D, Thorner J (2015) A Förster resonance energy transfer (FRET)-based system provides insight into the ordered assembly of yeast septin hetero-octamers. J. Biol. Chem. 290: 28388-28401. 

Muir A, Roelants FM, Timmons G, Leskoske KL, Thorner J (2015) Down-regulation of TORC2-Ypk1 signaling promotes MAPK-independent survival under hyperosmotic stress. Elife 4: 09336 (13pp).

Finnigan GC, Thorner J (2015) Complex in vivo ligation using homologous recombination and high-efficiency plasmid rescue from Saccharomyces cerevisiae. Bio-protocol 5: e1521 (14pp).

Finnigan GC, Booth EA, Duvalyan A, Liao EN, Thorner J (2015) The carboxy-terminal tails of septins Cdc11 and Shs1 recruit myosin-II binding factor Bni5 to the bud neck in Saccharomyces cerevisiae. Genetics 200: 843–862.

Finnigan GC, Takagi J, Cho C, Thorner J (2015) Comprehensive genetic analysis of paralogous terminal septin subunits Shs1 and Cdc11 in Saccharomyces cerevisiae. Genetics 200: 821–841.

Johnson CR, Weems AD, Brewer JM, Thorner J, McMurray MA (2015) Cytosolic chaperones mediate quality control of higher-order septin assembly in budding yeast. Mol. Biol. Cell 26: 1323-1344.

Roelants FM, Su BM, von Wulffen J, Ramachandran S, Sartorel E, Trott AE, Thorner J (2015) Protein kinase Gin4 negatively regulates flippase function and controls plasma membrane asymmetry. J. Cell Biol. 208: 299-311.    

O’Donnell AF, McCartney RR, Chandrashekarappa DG, Zhang BB, Thorner J, Schmidt MC (2015) 2-Deoxyglucose impairs Saccharomyces cerevisiae growth by stimulating Snf1-regulated and alpha-arrestin-mediated trafficking of hexose transporters 1 and 3. Mol. Cell. Biol. 35: 939-955.

Sartorel E, Barrey E, Lau RK, Thorner J (2015) Plasma membrane aminoglycerolipid flippase function is required for signaling competence in the yeast mating pheromone response pathway. Mol. Biol. Cell 26: 134-150.

Thorner J, Hunter T, Cantley LC, Sever R (2014) Signal transduction: from the atomic age to the post-genomic era. Cold Spring Harb. Perspect. Biol. 6: a022913.1-a022913.17.

Muir A, Ramachandran S, Roelants FM, Timmons G, Thorner J (2014) TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. eLIFE 3: e03779 (34pp.)

Cantley LC, Hunter T, Sever R, Thorner J (eds.) Signal Transduction: Principles, Pathways, and Processes.  Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 452pp., 2014.

Alvaro CG, O'Donnell AF, Prosser DC, Augustine AA, Goldman AR, Brodsky JL, Cyert MS, Wendland B, Thorner J (2014) Specific alpha-arrestins negatively regulate Saccharomyces cerevisiae pheromone response by down-modulating the G-protein coupled receptor Ste2. Mol. Cell. Biol. 34: 2660-2681.

O'Donnell AF, Huang L, Thorner J, Cyert MS (2013) A calcineurin-dependent switch controls the trafficking function of alpha-arrestin Aly1/Art6. J. Biol. Chem. 288: 24063-24080.

de Val N, McMurray MA, Lam LH, Hsiung C, Bertin A, Nogales E, Thorner J (2013)  Native cysteine residues are dispensable for the structure and function of all five yeast mitotic septins. Proteins 81: 1964-1979.

Konopka JB, Thorner JW (2013)  Pheromone Receptors (Yeast). In: Lennarz WJ, Lane MD (eds.) The Encyclopedia of Biological Chemistry, Vol. 3, pp. 441-446. Waltham, MA: Academic Press, Inc.

Lee YJ, Jeschke G, Roelants F, Thorner J, Turk B (2012) Reciprocal phosphorylation of yeast glycerol-3-phosphate dehydrogenases in adaptation to distinct types of stress.  Mol. Cell. Biol. 32: 4705-4717.

Wu H-J, Henzie J, Lin W-C, Rhodes C, Li Z, Sartorel E, Thorner J, Yang P, Groves JT (2012) Membrane-protein binding measured with solution-phase plasmonic nanocube sensors. Nature Methods 9: 1189-1191.

Bertin A, McMurray MA, Pierson J, Thai L, McDonald KL, Zehr EA, Garcia G 3rd, Peters P, Thorner J, Nogales E (2012) Three-dimensional ultrastructure of the septin filament network in Saccharomyces cerevisiae. Mol. Biol. Cell 23: 423-432.

Roelants FM, Breslow DK, Muir A, Weissman JS, Thorner J (2011)  Protein kinase Ypk1 phosphorylates Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiaeProc. Natl. Acad. Sci. USA 108: 19222-19227. 

Garcia G III, Bertin A, Li Z, Song Y, McMurray MA, Thorner J, Nogales E (2011) Subunit-dependent modulation of septin assembly: Budding yeast septin Shs1 promotes ring and gauze formation. J. Cell Biol. 195:  993-1004.

McMurray MA, Stefan CJ, Wemmer M, Odorizzi G, Emr SD, Thorner J (2011)  Genetic interactions with mutations affecting septin assembly reveal ESCRT functions in budding yeast cytokinesis.  Biol. Chem. 392: 699-712.

McMurray MA, Bertin A, Garcia G 3rd, Lam L, Nogales E, Thorner J (2011) Septin filament formation is essential in budding yeast.  Dev. Cell 20: 540-549. 
Lim S, Strahl T, Thorner J, Ames JB (2011)  Structure of a Ca2+-myristoyl switch protein that controls activation of a phosphatidylinositol 4-kinase in fission yeast.  J. Biol. Chem. 286: 12565-12577. 

Patterson JC, Klimenko ES, Thorner J (2010)  Single-cell analysis reveals that insulation maintains signaling specificity between two yeast MAPK pathways with common components. Sci. Sig. 3: ra75.1-ra75.11.

Bertin A, McMurray MA, Thai L,  Garcia G III, Votin V, Grob P, Allyn T, Thorner J, Nogales E (2010) Phosphatidylinositol-4,5-bisphosphate promotes budding yeast septin filament assembly and organization.          J. Mol. Biol. 404: 711-731.

Chen RE, Patterson JC, Goupil LS, Thorner J (2010)  Dynamic localization of Fus3 MAPK is necessary to evoke appropriate responses and avoid cytotoxic effects.  Mol. Cell. Biol. 30: 4293-4307.

Chen RE, Thorner J (2010)  Systematic epistasis analysis of the contributions of PKA- and MAPK-dependent signaling to nutrient limitation-evoked responses in the yeast Saccharomyces cerevisiaeGenetics 185: 855-870.

Garrenton LS, Stefan CJ, McMurray MA, Emr SD, Thorner J (2010)  Pheromone-induced anisotropy in yeast plasma membrane phosphatidylinositol-4,5-bisphosphate distribution is required for MAPK signaling.  Proc. Natl. Acad. Sci. USA 107: 11805-11810.

Roelants FM, Baltz AG, Trott AE, Fereres S, Thorner J (2010)  A protein kinase network regulates the function of aminophospholipid flippases. Proc. Natl. Acad. Sci. USA 107: 34-39.

Garrenton LS, Braunwarth A, Irniger S, Hurt E, Künzler M, Thorner J (2009)  Nucleus-specific and cell cycle-regulated degradation of mitogen-activated protein kinase scaffold protein Ste5 contributes to the control of signaling competence.  Mol. Cell. Biol. 29: 582-601.

McMurray MA, Thorner J (2009)  Septins: molecular partitioning and the generation of cellular asymmetry.  Cell Div. 4: 18.1-18.40.

McMurray MA, Thorner J (2009)  Reuse, replace, recycle. Specificity in subunit inheritance and assembly of higher-order septin structures during mitotic and meiotic division in budding yeast.  Cell Cycle 8: 195-203.

Rockwell NC, Wolfger H, Kuchler K, Thorner J (2009)  ABC transporter Pdr10 regulates the membrane microenvironment of Pdr12 in Saccharomyces cerevisiaeJ. Membr. Biol. 229: 27-52.

Westfall PJ, Patterson JC, Chen RE, Thorner J (2008) Stress resistance and signal fidelity independent of nuclear MAPK function.  Proc. Natl. Acad. Sci. USA 105: 12212-12217.

McMurray MA, Thorner J (2008)  Septin stability and recycling during dynamic structural transitions in cell division and development.  Curr. Biol. 18: 1203-1208.

McMurray MA, Thorner J (2008)  Biochemical properties and supramolecular architecture of septin hetero-oligomers and septin filaments, In "The Septins" (Hall PA, Russell SEG, Pringle JR, Eds.), John Wiley & Sons, Ltd., Chicester, West Sussex, UK, pp. 49-100.

Bertin A, McMurray MA, Grob P, Park SS, Garcia G 3rd, Patanwala I, Ng HL, Alber T, Thorner J, Nogales E (2008)  Saccharomyces cerevisiae septins: supramolecular organization of heterooligomers and the mechanism of filament assembly.  Proc. Natl. Acad. Sci. USA 105: 8274-8279.

Photo credit: Mark Hanson at Mark Joseph Studios.

Last Updated 2023-10-28