Publications

Tomko Lab Student Authors are Underlined Below.

PDF Betancourt, D. , Lawal, T .,  Tomko, R. J. Jr.,  Wiggle and Shake: Managing and Exploiting Conformational Dynamics during Proteasome Biogenesis.  Biomolecules  13(8), 1223, 2023  https://doi.org/10.3390/biom13081223

PDF       Nemec, A.A.,  Tomko, R. J. Jr.,  An unstructured proteasome inhibitor comes into focus. Journal of Biological Chemistry.299,9, 2023  https://doi.org/10.1016/j.jbc.2023.105145

PDF       Yanjie, L.,  Tomko, R. J. Jr., Hochstrasser, M., Proteasomes: Isolation and Activity Assays. Current Protocols.  https://doi.org/10.1002/cpz1.717

PDF Warnock, J.L., Jobin, G.W ., Kumar, S., and  Tomko, R. J. Jr.  Assembly chaperone Nas6 selectively destabilizes 26S proteasomes with defective regulatory particle-core particle interfaces. Journal of Biological Chemistry.299: 2, 2023  https://doi.org/10.1016/j.jbc.2023.102894

PDF Reed, R.G. , Jobin, G.W. , and  Tomko, R. J. Jr. Sem1/DSS1 accelerates ATP-dependent substrate unfolding by the proteasome through a conformation-dependent intercomplex contact. bioRxiv. h ttps://doi.org/10.1101/2022.06.27.497739

PDF       Huntsman, E.M., Cho, R.M., Kogan, H.V., McNamara-Bordewick, N.K.,  Tomko, R. J. Jr. , and Snow, J.W.  Proteasome inhibition is an effective treatment for Microsporidia infection in honey bees.  Biomolecules. 11:  1600, 2021. PMID: 34827599

PDF       Rossetti, M.L.,  Tomko, R. J. Jr., and Gordon, B.S.  Androgen depletion alters the diurnal patterns to signals that regulate autophagy in the limb skeletal muscle.  Molecular and Cellular Biochemistry. 476:  959-69, 2021. PMID: 33128669

PDF       Beesley, S., Kim, D.W., D'Alessandro, M., Jin, Y., Lee, K., Joo, H., Young, Y.,  Tomko, R. J. Jr. , Faulkner, J., Gamsby, J., Kim, J.K., and Lee, C.  Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis.  PNAS. 117:  28402-11, 2021. PMID: 33106420

PDF       Higgins, R., Kabbaj, M-H., Sherwin, D., Howell, L. A.,  Hatcher, A., Tomko, R. J. Jr., and Wang, Y.  The Cdc48 complex alleviates the cytotoxicity of misfolded proteins by regulating ubiquitin homeostasis.  Cell Reports. 32:  107898, 2020. PMID: 32668237

PDF       Nemec, A. A. and  Tomko, R. J. Jr. A suite of polymerase chain reaction-based peptide tagging plasmids for epitope-targeted enzymatic functionalization of yeast proteins.  Yeast. 37:  327-35, 2020. PMID: 32401365.

PDF Howell, L. A. , Peterson, A. K., and  Tomko, R. J. Jr. Proteasome subunit Alpha1 overexpression preferentially drives canonical proteasome biogenesis and enhances stress tolerance in yeast.  Scientific Reports. 9:  12418, 2019. PMID: 31455793.

PDF       Rosetti, M. L., Esser, K. A., Lee, C.,  Tomko, R. J. Jr., Eroshkin, A. M., and Gordon, B.S.  Disruptions to the Limb Muscle Core Molecular Clock Coincide with Changes in Mitochondrial Quality Control following Androgen Depletion.  American Journal of Physiology, Endocrinology, and Metabolism. 317:  E631-E645, 2019. PMID: 31361545.

PDF Reed, R. G.  and  Tomko, R. J. Jr. Engineered disulfide crosslinking to measure conformational changes in the 26S proteasome.  Methods in Enzymology. 619: 145-159, 2019. PMID: 30910019.

PDF       Koch, B. A., Jin, H.,  Tomko, R. J. Jr., and Yu, H. G. The anaphase-promoting complex regulates degradation of the inner nuclear membrane protein Mps3.  Journal of Cell Biology. 218: 839-854, 2019.  PMID:   30737264. 

PDF       Nemec, A. A., Peterson A. K., Warnock, J. L., Reed, R. G. , and  Tomko, R. J. Jr. An Allosteric Interaction Network Promotes Conformation State-Dependent Eviction of the Nas6 Assembly Chaperone from Nascent 26S Proteasomes.  Cell Reports. 26: 483-495, 2019. PMID: 30625330.

PDF       Eisele, M.†,  Reed, R. G. †, Rudack, T.†, Schweitzer, A., Beck, F., Nagy, I., Pfeifer, G., Plitzko, J., Baumeister, W.,*  Tomko, R. J. Jr.,*# and Sakata, E.* Expanded coverage of the 26S proteasome conformational landscape reveals mechanisms of peptidase gating.  Cell Reports. 24: 1301-1315, 2018. PMID: 30067984.
                           †Equal contributions 
*Corresponding author
#Lead contact
Featured in  Trends in Biochemical Sciences  2018; 18: 30150-6.

PDF       Nemec, A. A.,* Howell, L. A. ,* Peterson, A. K., Murray, M. A. , and Tomko, R. J. Jr.  Autophagic clearance of proteasomes in yeast requires the conserved sorting nexin Snx4.  Journal of Biological Chemistry.  292: 21466-21480, 2017.   PMID: 29109144. 
                           *Equal contributions

PDF Tomko, Jr., R.J. Proteasomes, Caught In the Act.   Cell Research. 27:  307-308, 2017.  

PDF Howell, L. A. , Tomko, R. J. Jr.*, and Kusmierczyk, A. R.* Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis. Frontiers in Biology.12: 19-48, 2017.
*Corresponding Author

PDF Tomko, Jr., R.J.,* Taylor, D.W., Chen, Z.A., Wang, H.W., Rappsilber, J., and Hochstrasser, M.  A Single Alpha Helix Drives Largescale Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly.   Cell. 163: 432-444, 2015.  
*Corresponding Author

PDF        Li, Y., Tomko, Jr., R.J., and Hochstrasser, M.  Proteasomes: Isolation and activity assays.   Curr. Protoc. Cell Biol.67:3.43.1-3.43.20, 2015.

PDF Tomko, R. J. Jr.and Hochstrasser, M.  The Intrinsically Disordered Sem1 Protein Functions as a Molecular Tether During Proteasome Lid Biogenesis. Molecular Cell. 53: 433–443, 2014.

PDF       Sá-Moura, B., Funakoshi, M., Tomko, R. J. Jr., Dohmen, J., Wu, Z., Peng, J., and Hochstrasser, M. A Conserved Protein with AN1 Zinc-finger and Ubiquitin-like Domains Modulates Cdc48 (p97) Function in the Ubiquitin-Proteasome Pathway. Journal of Biological Chemistry. 288: 33682-96, 2013.

PDF Tomko, R. J. Jr. and Hochstrasser, M. Molecular Architecture and Assembly of the Eukaryotic Proteasome. Annual Review of Biochemistry. 82: 415-45, 2013.

PDF Tomko, R. J. Jr.and Hochstrasser, M. Incorporation of the Rpn12 Subunit Couples Completion of Proteasome Regulatory Particle Lid Assembly to Lid-Base Joining. Molecular Cell. 44: 907-917, 2011.

PDF Tomko, R. J. Jr.and Hochstrasser, M. Order of the proteasomal ATPases and eukaryotic proteasome assembly. Cell Biochemistry & Biophysics. 60: 13-20, 2011.

PDF       Heinemann, I., Randau, L., Tomko, R. J. Jr., and Söll, D. 3’-5’ tRNAHis guanylyltransferase in bacteria. FEBS Letters. 584: 3567-3572, 2010.

PDF Tomko, R. J. Jr., Funakoshi, M., Schneider, K., Wang, J., and Hochstrasser, M. Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly. Molecular Cell. 38: 393-403, 2010.
*Featured in: Mol. Cell. 2010; 38: 319-20.
*Recommended by Faculty of 1000

PDF       Wang, P., Zou, F., Zhang, X., Tomko, R. J. Jr., Lazo, J. S., Wang, Z., Zhang, L., and Yu, J. MicroRNA-21 modulates G2/M checkpoint and cell cycle progression through Cdc25A. Cancer Research. 69: 8157-65, 2009.

PDF       Funakoshi, M., Tomko, R. J. Jr., Kobyashi, H., and Hochstrasser, M. Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base. Cell. 137: 887-899, 2009.
*Featured in: Cell. 2009; 138:25-8.
*Featured in: Nature Reviews Molecular Cell Biology. 2009; 10:442-3.
*Featured in: Biopolymers. 9: iii, 2009.
*Recommended by Faculty of 1000

PDF Tomko, R. J. Jr., Azang-Njaah, N. N., and Lazo, J. S. Nitrosative stress suppresses checkpoint activation after DNA synthesis inhibition. Cell Cycle. 8: 299-305, 2009.

PDF Tomko, R. J. Jr., and Lazo, J. S. Multimodal control of Cdc25A by nitrosative stress. Cancer Research. 68: 7457-7465, 2008.

PDF       Queiroz de Oliveira, P. E., Tomko, R. J. Jr., and Lazo, J. S. Is a step backwards in S-phase-targeted chemotherapy a step forward? Molecular Interventions. 8: 137-40, 2008.
*Cover article

PDF       Brisson, M., Foster, C., Wipf, P., Joo, B., Tomko, R. J. Jr., Nguyen, T., and Lazo, J. S. Independent mechanistic inhibition of Cdc25 phosphatases by a natural product caulibugulone. Molecular Pharmacology. 71: 184-92, 2007.

PDF Tomko, R. J. Jr., Bansal, P., and Lazo, J. S. Airing out an antioxidant role for the tumor suppressor p53. Molecular Interventions. 6: 23-25, 2006.

PDF       Aponick, A., Buzdygon, R. S., Tomko, R. J. Jr., Fazal, A. N., Shughart, E. L., McMaster, D. M., Meyers, M. C., Pitcock, W. H. Jr., and Wigal, C. T. Regioselective organocadmium alkylations of substituted quinones. Journal of Organic Chemistry. 67: 242-244, 2002.