Please click here to read Dr. Alexander Varshavsky's 2006 interview with Prof. I. Hargittai in Candid Science.
Main Research Interests: The ubiquitin system; the N-end rule pathway; new approaches to cancer therapy
Lab's History and Current Studies
We are interested in just about everything. But the brevity of life being what it is compels selectivity. Hence our main subject – the ubiquitin system – chosen partly by preference and partly by accident.
The field of ubiquitin and regulated protein degradation was created in the 1980s, largely through the complementary discoveries by the laboratory of A. Hershko (Technion, Haifa, Israel) and by my laboratory, then at MIT. These discoveries revealed three sets of previously unknown facts:
- That ATP-dependent protein degradation involves a new protein modification, ubiquitin conjugation, which is mediated by specific enzymes, termed E1, E2 and E3.
- That the selectivity of ubiquitin conjugation is determined by specific degradation signals (degrons) in short-lived proteins, including the degrons that give rise to the N end rule.
- That ubiquitin-dependent processes play a strikingly broad, previously unsuspected part in cellular physiology, primarily by controlling the in vivo levels of specific proteins. My laboratory has shown that ubiquitin conjugation is required for the protein degradation in vivo, for cell viability, and also, specifically, for the cell cycle, DNA repair, protein synthesis, transcriptional regulation, and stress responses. We also cloned and analyzed the first ubiquitin genes, the first specific E3 ubiquitin ligase (UBR1), the first deubiquitylating enzymes (UBP1 and UBP2), and identified the first physiological substrate of the ubiquitin system, the MATalpha2 transcriptional repressor. We showed that ubiquitin-dependent proteolysis involves a polyubiquitin chain of unique topology that is required for protein degradation. We also discovered that the ubiquitin system is capable of subunit selectivity, i.e., it can destroy a specific subunit of a multisubunit protein, leaving the rest of the protein intact and thereby making possible protein remodeling. This fundamental process underlies the cell cycle (replacement of cyclin subunits in cell-cycle kinases), the activation of transcription factors such as, for example, NF-kappaB, and many other processes. Together, these biological (function-based) studies in the 1980s resulted in the overall discovery of physiological regulation by intracellular protein degradation.
The Hershko laboratory produced the first of three fundamental advances, in 1978-1983 (item 1), and my laboratory produced the other two, in 1984-1990 (items 2 and 3).
The above complementary insights led to enormous expansion of the ubiquitin field in the 1990s and afterward. This field is now one of the largest arenas in biomedical science, the point of convergence of many disparate disciplines.
My lab's biological discoveries in the 1980s yielded the modern paradigm of the central importance of regulated proteolysis for the control of the levels of specific proteins in vivo, as distinguished from their control by transcription and protein synthesis. In other words, these advances revealed that the control through regulated protein degradation rivals, and often surpasses in significance the classical regulation through transcription and translation.
This radically changed understanding of the design of biological circuits has major ramifications for medicine, given the astounding functional range of the ubiquitin system and the multitude of ways in which ubiquitin-dependent processes can malfunction in disease or in the course of aging, from cancer and neurodegenerative syndromes to perturbations of immunity and many other illnesses, including birth defects.
For accounts of the early history of the ubiquitin field, see:
Hershko, Ciechanover and Varshavsky (2000) The ubiquitin system. Nature Medicine 6, 1073-1081;
Varshavsky (2006) The early history of the ubiquitin field. Protein Science 15, 647-654.
My laboratory continues to study ubiquitin-dependent processes, with a focus on the N-end rule pathway of protein degradation, which we analyze in the mouse, in the yeast Saccharomyces cerevisiae, and in prokaryotes. The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Although prokaryotes lack the ubiquitin system, the N-end rule pathway (its ubiquitin-independent versions) is present in them as well.
We are also interested in developing new approaches to therapy of currently intractable diseases, particularly cancer. For recent ideas in this area that we are working on in the lab, see Varshavsky (2007) Targeting the absence: homozygous DNA deletions as immutable signposts for cancer therapy. Proc. Natl. Acad. Sci. USA 104, 14935-14940.
Turner, G. C. and Varshavsky, A. (2000) Detecting and measuring cotranslational protein degradation in vivo. Science 289, 2117-2120.
Xie, Y. and Varshavsky, A. (2000) Physical association of ubiquitin ligases and the 26S proteasome. Proc. Natl. Acad. Sci. USA 97, 2497-2502.
Kwon, Y. T., Balogh, S. A., Davydov, I. V., Kashina, A. S., Yoon, J. K., Xie, Y., Gaur, A., Hyde, L., Denenberg, V. H. and Varshavsky, A. (2000) Altered activity, social behavior, and spatial memory in mice lacking the NTAN1p amidase and the asparagine branch of the N-end rule pathway. Mol. Cell. Biol. 20, 4135-4148.
Turner, G. C., Du, F. and Varshavsky, A. (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 405, 579-583.
Davydov, I. V. and Varshavsky, A. (2000) RGS4 is arginylated and degraded by the N-end rule pathway in vitro. J. Biol. Chem. 275, 22931-22941.
Hershko, A., Ciechanover, A. and Varshavsky, A. (2000) The ubiquitin system. Nature Medicine 6, 1073-1081.
Rao, H., Uhlmann, F., Nasmyth, K. and Varshavsky, A. (2001) Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability. Nature 410, 955-960.
Xie, Y. and Varshavsky, A. (2001) RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc. Natl. Acad. Sci. USA 98, 3056-3061.
Kwon, Y. T., Xia, Z.-X., Davydov, I. V., Lecker, S. H. and Varshavsky, A. (2001) Construction and analysis of mouse strains lacking the ubiquitin ligase UBR1 of the N-end rule pathway. Mol. Cell. Biol. 21, 8007-8021.
Kwon, Y. T., Kashina, A. S., Davydov, I. V., Hu, R.-G., An, J. Y., Seo, J. W., Du, F. and Varshavsky, A. (2002) An essential role of N-terminal arginylation in cardiovascular development. Science 297, 96-99.
Du, F., Navarro-Garcia, F. Xia, Z., Tasaki, T. and Varshavsky, A. (2002) Pairs of dipeptides activate the binding of substrate by ubiquitin ligase through dissociation of its autoinhibitory domain. Proc. Natl. Acad. Sci. USA 99, 14110-14115.
Sheng, J., Kumagai, A., Dunphy, W. and Varshavsky, A. (2002) Dissection of c-MOS degron. EMBO J. 21, 6061-6071.
Xie, Y. and Varshavsky, A. (2002) The UFD4 ubiquitin ligase lacking the proteasome-binding region catalyzes ubiquitylation but is impaired in proteolysis. Nature Cell Biol. 4, 1003-1007.
Varshavsky, A. (2003) The N-end rule and regulation of apoptosis. Nature Cell Biol. 5, 373-376.
Kwon, Y. T., Xia, Z., An, J. Y., Tasaki, T., Davydov, I. V., Seo, J. W., Sheng, J., Xie, Y. and Varshavsky, A. (2003) Female lethality and apoptosis of spermatocytes in mice lacking the UBR2 ubiquitin ligase of the N-end rule pathway. Mol. Cell. Biol. 23, 8255-8271.
Varshavsky, A. (2004) Spalog and sequelog: neutral terms for spatial and sequence similarity. Curr. Biol. 14, R181-R183.
Varshavsky, A. (2005) Regulated protein degradation. Trends Biochem. Sci. 6, 283-286.
Tasaki, T., Mulder, L. C. F., Iwamatsu, A., Lee, M. J., Davydov, I. V., Varshavsky, A., Muesing, M. and Kwon, Y. T. (2005) A family of mammalian E3 ubiquitin ligases that contain the UBR motif and recognize N-degrons. Mol. Cell. Biol. 25, 7120-7136.
Hu, R.G., Sheng, J., Qi, X., Xu, Z., Takahashi, T. T. and Varshavsky, A. (2005) The N-end rule pathway as a nitric oxide sensor controlling the levels of multiple regulators. Nature 473, 981-986.
Zenker, M, Mayerle, J., Lerch, M. M., Tagariello, A., Zerres, K., Durie, P. R., Beier, M., Hülskamp, G., Guzman, C., Rehder, H., Beemer, F. A., Hamel, B., Vanlieferinghen, P., Gershoni-Baruch, R., Vieira, M. W., Dumic, M., Auslender, R., Gil-da-Silva-Lopes, V. L., Steinlicht, S., Rauh, M., Shalev, S. A., Thiel, C., Ekici, A. B., Winterpacht, A., Kwon, Y. T., Varshavsky, A. and Reis, A. (2005) Deficiency of UBR1, a ubiquitin ligase of the N-end rule pathway, causes pancreatic dysfunction, malformations and mental retardation (Johanson-Blizzard syndrome). Nature Genet. 37, 1345-1350.
Graciet, E. Hu, R. G., Piatkov, K., Rhee, J. H., Schwarz, E. M. and Varshavsky, A. (2006) Aminoacyl-transferases and the N-end rule pathway of prokaryotic/eukaryotic specificity in a human pathogen. Proc. Natl. Acad. Sci. USA 103, 3078-3083.
An, J. Y., Seo, J. W., Tasaki, T., Lee, M. J., Varshavsky, A., Kwon, Y. T. (2006) Impaired neurogenesis and cardiovascular development in mice lacking the E3 ubiquitin ligases UBR1 and UBR2 of the N-end rule pathway. Proc. Natl. Acad. Sci. USA 103, 6212-6217.
Varshavsky, A. (2006) The early history of the ubiquitin field. Protein Science 15, 647-654.
Hu, R.-G., Brower, C. S., Wang, H., Davydov, I. V, Sheng, J., Zhou, J., Kwon, Y. T. and Varshavsky, A. (2006) Arginyl-transferase, its specificity, putative substrates, bidirectional promoter, and splicing-derived isoforms. J. Biol. Chem. 281, 32559-32573.
Tasaki, T., Sohr, R., Hellweg, R., Hortnagl, H., Varshavsky, A. and Kwon, Y. T. (2007) Biochemical and Genetic Studies of UBR3, a Ubiquitin Ligase with a Function in Olfactory and Other Sensory Systems. J. Biol. Chem. 282, 18510-18520.
Varshavsky, A. (2007) Targeting the absence: homozygous DNA deletions as immutable signposts for cancer therapy. Proc. Natl. Acad. Sci. USA 104, 14935-14940.
Schnupf, P., Zhou, J., Varshavsky, A. and Portnoy, D. A. (2007) Listeriolysin O secreted by Listeria monocytogenes into the host cell cytosol is degraded by the N-end rule pathway. Infection & Immunity 75, 5135-5147.
Connor, R.E., Piatkov, K.P., Varshavsky, A., Tirrell, D.A. (2007) Enzymatic N-terminal addition of noncanonical amino acids to peptides and proteins. ChemBioChem. (in press).
Hu, R.-G., Wang, H., Xia, Z. and Varshavsky, A. (2008) The N-end rule pathway is a sensor of heme. Proc. Natl. Acad. Sci. USA (in press).