Enzymes; Molecular Biology; Saccharomyces cerevisiae; Mass Spectrometry; Transcription Factors; Microscopy, Immunoelectron; Gene Deletion; Ubiquitin; Cell Growth Processes; Mutant Chimeric Proteins
Molecular Biophysics and Biochemistry: Hochstrasser Lab
We wish to understand at a molecular level how specific eukaryotic proteins are selected for rapid degradation even while most proteins are spared. Such turnover occurs primarily through the ubiquitin-proteasome system and is central to a variety of cell regulatory mechanisms, many of medical relevance. The proteasome is a molecular machine that fragments proteins into short peptides. More generally, we study the reversible enzymatic coupling of proteins to other proteins within cells. The prototypical example of such a protein modifier is ubiquitin, but at least a dozen such systems exist. While ubiquitin generally is used to mark its targets for destruction, the consequences of protein ligation to the various “ubiquitin-like proteins” are less understood. One such protein that we study, SUMO, is attached to many proteins and is crucial for cell-cycle progression. Much of our work is conducted in baker’s yeast, a model organism ideal for genetic and biochemical analysis.
Speciailzed Terms: Adenosinetriphosphatase; Cell Growth Regulation; Chemical Cleavage; Chemical Conjugate; Chimeric Protein; Enzyme Activity; Enzyme Complex; Enzyme Mechanism; Enzyme Structure; Fungal Genetics; Gene Deletion Mutation; Immunoelectron Microscopy; Isozyme; Mass Spectrometry; Mutant; Proteasome; Protein Degradation; Protein Purification; Proteinase; Protooncogene; Saccharomyces Cerevisiae; Transcription Factor; Ubiquitin
Extensive Research Description
Our lab has as its general focus one of the fundamental regulatory systems of eukaryotic cells – the ubiquitin system. Ubiquitin and an array of related molecules (ubiquitin-like proteins or Ubls) such as SUMO are small, highly conserved proteins that are covalently attached to other intracellular proteins, resulting in various functional alterations of these targets. The ubiquitin system has only recently come under close scrutiny, and an extraordinary array of cell regulatory functions is gradually being uncovered. Moreover, many links are now being found between defects in this pathway and human disease, including many cancers, developmental abnormalities, Parkinson’s disease, Alzheimer’s disease, and certain severe forms of mental retardation.
The research in our laboratory can be grouped into two broad and overlapping areas. First, we wish to understand, at a mechanistic and molecular level, how specific proteins are rapidly degraded within eukaryotic cells while most proteins are spared. Such turnover is central to a great variety of regulatory mechanisms, including many of medical relevance. Much of this regulated degradation occurs via the highly conserved ubiquitin-proteasome system. We are currently studying a transmembrane ubiquitin ligase that resides in the nuclear envelope and endoplasmic reticulum. This ligase attaches ubiquitin to both nuclear regulatory proteins and to misfolded membrane proteins degraded at the ER (ER-associated degradation or ERAD). The proteasome is a large, cylindrical machine that fragments proteins into short peptides. Our primary current interest with the proteasome is its mechanism of assembly.
In our second major area of research, we are analyzing the function and dynamics of protein modification by other Ubls. The prototypical example of a protein that is covalently attached to other proteins is ubiquitin, but in recent years, evidence for at least a dozen such systems has come to light. While ubiquitin generally is used to mark its targets for destruction, the consequences of protein ligation to the various Ubls are poorly understood. The Ubl called SUMO is attached to many proteins in vivo and is crucial for cell-cycle progression. We discovered the first enzymes that can remove SUMO from other proteins, causing this protein modification to be highly dynamic. We are trying to understand the functional consequences of SUMO-protein modification, particularly in cell cycle checkpoints, and to determine the basis of specificity for the SUMO-cleaving proteases. Much of our work is conducted in the yeast Saccharomyces cerevisiae, an organism that permits both facile genetic manipulation and detailed biochemical analysis.
A multimeric assembly factor controls formation of alternative 20S proteasomes.
Kusmierczyk, A., Kunjappu, M. J., Funakoshi, M. and Hochstrasser, M. A multimeric assembly factor controls formation of alternative 20S proteasomes. Nature Struct. Mol. Biol. 15, 237-244 (2008)
Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue.
Ravid, T. and Hochstrasser, M. (2007). Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue. Nat. Cell Biol. 9:422-427.
Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase.
Deng, M. and Hochstrasser, M. (2006). Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase. Nature 443:827-831.
A nuclear envelope protein linking nuclear pore basket assembly, SUMO protease regulation, and mRNA surveillance.
Lewis, A., Felberbaum, R. and Hochstrasser, M. A nuclear envelope protein linking nuclear pore basket assembly, SUMO protease regulation, and mRNA surveillance. J. Cell Biol. 178, 813-827 (2007)
b-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint.
Li, X., Kusmierczyk, A., Wong, P., Emili, A. and Hochstrasser, M. b-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. EMBO J. 26, 2339-2349 (2007)
Full List of PubMed Publications
- Ryu HY, Hochstrasser M: Adaptive aneuploidy counters a dysregulated SUMO system. Cell Cycle. 2017 Mar 4; 2016 Nov 18. PMID: 27860533
- Beckmann JF, Ronau JA, Hochstrasser M: A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility. Nat Microbiol. 2017 Mar 1; 2017 Mar 1. PMID: 28248294
- Hochstrasser M: Gyre and gimble in the proteasome. Proc Natl Acad Sci U S A. 2016 Nov 15; 2016 Nov 3. PMID: 27810957
- Ryu HY, Wilson NR, Mehta S, Hwang SS, Hochstrasser M: Loss of the SUMO protease Ulp2 triggers a specific multichromosome aneuploidy. Genes Dev. 2016 Aug 15; 2016 Sep 1. PMID: 27585592
- Berk JM, Hochstrasser M: Protein Modification: Bacterial Effectors Rewrite the Rules of Ubiquitylation. Curr Biol. 2016 Jul 11. PMID: 27404243
- Zattas D, Berk JM, Kreft SG, Hochstrasser M: A Conserved C-terminal Element in the Yeast Doa10 and Human MARCH6 Ubiquitin Ligases Required for Selective Substrate Degradation. J Biol Chem. 2016 Jun 3; 2016 Apr 11. PMID: 27068744
- Hu R, Hochstrasser M: Recent progress in ubiquitin and ubiquitin-like protein (Ubl) signaling. Cell Res. 2016 Apr. PMID: 27033807
- Ronau JA, Beckmann JF, Hochstrasser M: Substrate specificity of the ubiquitin and Ubl proteases. Cell Res. 2016 Apr; 2016 Mar 25. PMID: 27012468
- Gillies J, Hickey CM, Su D, Wu Z, Peng J, Hochstrasser M: SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus in Saccharomyces cerevisiae. Genetics. 2016 Apr; 2016 Feb 2. PMID: 26837752
- Padmanabhan A, Vuong SA, Hochstrasser M: Assembly of an Evolutionarily Conserved Alternative Proteasome Isoform in Human Cells. Cell Rep. 2016 Mar 29; 2016 Mar 22. PMID: 26997268
- Huber EM, Heinemeyer W, Li X, Arendt CS, Hochstrasser M, Groll M: A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun. 2016 Mar 11; 2016 Mar 11. PMID: 26964885
- Li X, Li Y, Arendt CS, Hochstrasser M: Distinct Elements in the Proteasomal β5 Subunit Propeptide Required for Autocatalytic Processing and Proteasome Assembly. J Biol Chem. 2016 Jan 22; 2015 Dec 1. PMID: 26627836
- Wilson NR, Hochstrasser M: The Regulation of Chromatin by Dynamic SUMO Modifications. Methods Mol Biol. 2016. PMID: 27631795
- Tomko RJ Jr, Taylor DW, Chen ZA, Wang HW, Rappsilber J, Hochstrasser M: A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly. Cell. 2015 Oct 8. PMID: 26451487
- Hickey CM, Hochstrasser M: STUbL-mediated degradation of the transcription factor MATα2 requires degradation elements that coincide with corepressor binding sites. Mol Biol Cell. 2015 Oct 1; 2015 Aug 5. PMID: 26246605
- Li Y, Tomko RJ Jr, Hochstrasser M: Proteasomes: Isolation and Activity Assays. Curr Protoc Cell Biol. 2015 Jun 1; 2015 Jun 1. PMID: 26061243
- Zattas D, Hochstrasser M: Ubiquitin-dependent protein degradation at the yeast endoplasmic reticulum and nuclear envelope. Crit Rev Biochem Mol Biol. 2015 Jan-Feb; 2014 Sep 18. PMID: 25231236
- Kang H, Bradley MJ, Cao W, Zhou K, Grintsevich EE, Michelot A, Sindelar CV, Hochstrasser M, De La Cruz EM: Site-specific cation release drives actin filament severing by vertebrate cofilin. Proc Natl Acad Sci U S A. 2014 Dec 16; 2014 Dec 2. PMID: 25468977
- Tomko RJ Jr, Hochstrasser M: The intrinsically disordered Sem1 protein functions as a molecular tether during proteasome lid biogenesis. Mol Cell. 2014 Feb 6; 2014 Jan 9. PMID: 24412063
- Kunjappu MJ, Hochstrasser M: Assembly of the 20S proteasome. Biochim Biophys Acta. 2014 Jan; 2013 Mar 16. PMID: 23507199
- Sá-Moura B, Funakoshi M, Tomko RJ Jr, Dohmen RJ, Wu Z, Peng J, Hochstrasser M: A conserved protein with AN1 zinc finger and ubiquitin-like domains modulates Cdc48 (p97) function in the ubiquitin-proteasome pathway. J Biol Chem. 2013 Nov 22; 2013 Oct 11. PMID: 24121501
- Zattas D, Adle DJ, Rubenstein EM, Hochstrasser M: N-terminal acetylation of the yeast Derlin Der1 is essential for Hrd1 ubiquitin-ligase activity toward luminal ER substrates. Mol Biol Cell. 2013 Apr; 2013 Jan 30. PMID: 23363603
- Tomko RJ Jr, Hochstrasser M: Molecular architecture and assembly of the eukaryotic proteasome. Annu Rev Biochem. 2013; 2013 Mar 13. PMID: 23495936
- Hickey CM, Wilson NR, Hochstrasser M: Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol. 2012 Dec. PMID: 23175280
- Rubenstein EM, Kreft SG, Greenblatt W, Swanson R, Hochstrasser M: Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase. J Cell Biol. 2012 Jun 11. PMID: 22689655
- Gillies J, Hochstrasser M: A new class of SUMO proteases. EMBO Rep. 2012 Apr 2; 2012 Apr 2. PMID: 22422001
- Hochstrasser M, Funakoshi M: Disulfide engineering to map subunit interactions in the proteasome and other macromolecular complexes. Methods Mol Biol. 2012. PMID: 22350897
- Felberbaum R, Wilson NR, Cheng D, Peng J, Hochstrasser M: Desumoylation of the endoplasmic reticulum membrane VAP family protein Scs2 by Ulp1 and SUMO regulation of the inositol synthesis pathway. Mol Cell Biol. 2012 Jan; 2011 Oct 24. PMID: 22025676
- Tomko RJ Jr, Hochstrasser M: Incorporation of the Rpn12 subunit couples completion of proteasome regulatory particle lid assembly to lid-base joining. Mol Cell. 2011 Dec 23. PMID: 22195964
- Kreft SG, Hochstrasser M: An unusual transmembrane helix in the endoplasmic reticulum ubiquitin ligase Doa10 modulates degradation of its cognate E2 enzyme. J Biol Chem. 2011 Jun 10; 2011 Apr 5. PMID: 21467040
- Tomko RJ Jr, Hochstrasser M: Order of the proteasomal ATPases and eukaryotic proteasome assembly. Cell Biochem Biophys. 2011 Jun. PMID: 21461838
- Kusmierczyk AR, Kunjappu MJ, Kim RY, Hochstrasser M: A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding. Nat Struct Mol Biol. 2011 May; 2011 Apr 17. PMID: 21499243
- Rubenstein EM, Hochstrasser M: Redundancy and variation in the ubiquitin-mediated proteolytic targeting of a transcription factor. Cell Cycle. 2010 Nov 1; 2010 Nov 22. PMID: 20980825
- Su D, Hochstrasser M: A WLM protein with SUMO-directed protease activity. Mol Cell Biol. 2010 Aug; 2010 Jun 21. PMID: 20566698
- Tomko RJ Jr, Funakoshi M, Schneider K, Wang J, Hochstrasser M: Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly. Mol Cell. 2010 May 14. PMID: 20471945
- Xie Y, Rubenstein EM, Matt T, Hochstrasser M: SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor. Genes Dev. 2010 May; 2010 Apr 13. PMID: 20388728
- Funakoshi M, Tomko RJ Jr, Kobayashi H, Hochstrasser M: Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base. Cell. 2009 May 29; 2009 May 14. PMID: 19446322
- Kroetz MB, Su D, Hochstrasser M: Essential role of nuclear localization for yeast Ulp2 SUMO protease function. Mol Biol Cell. 2009 Apr; 2009 Feb 18. PMID: 19225149
- Hochstrasser M: Origin and function of ubiquitin-like proteins. Nature. 2009 Mar 26. PMID: 19325621
- Funakoshi M, Hochstrasser M: Small epitope-linker modules for PCR-based C-terminal tagging in Saccharomyces cerevisiae. Yeast. 2009 Mar. PMID: 19243080
- Kroetz MB, Hochstrasser M: Identification of SUMO-interacting proteins by yeast two-hybrid analysis. Methods Mol Biol. 2009. PMID: 19107413
- Wang L, Dong H, Soroka CJ, Wei N, Boyer JL, Hochstrasser M: Degradation of the bile salt export pump at endoplasmic reticulum in progressive familial intrahepatic cholestasis type II. Hepatology. 2008 Nov. PMID: 18798335
- Kusmierczyk AR, Hochstrasser M: Some assembly required: dedicated chaperones in eukaryotic proteasome biogenesis. Biol Chem. 2008 Sep. PMID: 18713001
- Kusmierczyk AR, Kunjappu MJ, Funakoshi M, Hochstrasser M: A multimeric assembly factor controls the formation of alternative 20S proteasomes. Nat Struct Mol Biol. 2008 Mar; 2008 Feb 17. PMID: 18278055
- Felberbaum R, Hochstrasser M: Ulp2 and the DNA damage response: desumoylation enables safe passage through mitosis. Cell Cycle. 2008 Jan 1; 2007 Oct 28. PMID: 18196960
- Xie Y, Kerscher O, Kroetz MB, McConchie HF, Sung P, Hochstrasser M: The yeast Hex3.Slx8 heterodimer is a ubiquitin ligase stimulated by substrate sumoylation. J Biol Chem. 2007 Nov 23; 2007 Sep 11. PMID: 17848550
- Schwartz DC, Felberbaum R, Hochstrasser M: The Ulp2 SUMO protease is required for cell division following termination of the DNA damage checkpoint. Mol Cell Biol. 2007 Oct; 2007 Jul 30. PMID: 17664284
- Lewis A, Felberbaum R, Hochstrasser M: A nuclear envelope protein linking nuclear pore basket assembly, SUMO protease regulation, and mRNA surveillance. J Cell Biol. 2007 Aug 27. PMID: 17724121
- Hochstrasser M: Ubiquitin ligation without a ligase. Dev Cell. 2007 Jul. PMID: 17609103
- Li X, Kusmierczyk AR, Wong P, Emili A, Hochstrasser M: beta-Subunit appendages promote 20S proteasome assembly by overcoming an Ump1-dependent checkpoint. EMBO J. 2007 May 2; 2007 Apr 12. PMID: 17431397
- Ravid T, Hochstrasser M: Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue. Nat Cell Biol. 2007 Apr; 2007 Feb 21. PMID: 17310239
- Deng M, Hochstrasser M: Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase. Nature. 2006 Oct 19. PMID: 17051211
- Arteaga MF, Wang L, Ravid T, Hochstrasser M, Canessa CM: An amphipathic helix targets serum and glucocorticoid-induced kinase 1 to the endoplasmic reticulum-associated ubiquitin-conjugation machinery. Proc Natl Acad Sci U S A. 2006 Jul 25; 2006 Jul 17. PMID: 16847254
- Hochstrasser M, Cohen R: Cecile M. Pickart 1954-2006. Nat Cell Biol. 2006 Jun. PMID: 16738698
- Kreft SG, Wang L, Hochstrasser M: Membrane topology of the yeast endoplasmic reticulum-localized ubiquitin ligase Doa10 and comparison with its human ortholog TEB4 (MARCH-VI). J Biol Chem. 2006 Feb 24; 2005 Dec 22. PMID: 16373356
- Ravid T, Kreft SG, Hochstrasser M: Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways. EMBO J. 2006 Feb 8; 2006 Jan 26. PMID: 16437165
- Hochstrasser M: Lingering mysteries of ubiquitin-chain assembly. Cell. 2006 Jan 13. PMID: 16413479
- Kerscher O, Felberbaum R, Hochstrasser M: Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol. 2006. PMID: 16753028
- Hannich JT, Lewis A, Kroetz MB, Li SJ, Heide H, Emili A, Hochstrasser M: Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem. 2005 Feb 11; 2004 Dec 6. PMID: 15590687
- Amerik AY, Hochstrasser M: Mechanism and function of deubiquitinating enzymes. Biochim Biophys Acta. 2004 Nov 29. PMID: 15571815
- Ravid T, Hochstrasser M: NF-kappaB signaling: flipping the switch with polyubiquitin chains. Curr Biol. 2004 Oct 26. PMID: 15498483
- Velichutina I, Connerly PL, Arendt CS, Li X, Hochstrasser M: Plasticity in eucaryotic 20S proteasome ring assembly revealed by a subunit deletion in yeast. EMBO J. 2004 Feb 11; 2004 Jan 22. PMID: 14739934
- Laney JD, Hochstrasser M: Ubiquitin-dependent degradation of the yeast Mat(alpha)2 repressor enables a switch in developmental state. Genes Dev. 2003 Sep 15; 2003 Sep 2. PMID: 12952895
- Schwartz DC, Hochstrasser M: A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem Sci. 2003 Jun. PMID: 12826404
- Li SJ, Hochstrasser M: The Ulp1 SUMO isopeptidase: distinct domains required for viability, nuclear envelope localization, and substrate specificity. J Cell Biol. 2003 Mar 31; 2003 Mar 24. PMID: 12654900
- Laney JD, Hochstrasser M: Analysis of protein ubiquitination. Curr Protoc Protein Sci. 2002 Nov. PMID: 18429222
- Hochstrasser M: Molecular biology. New proteases in a ubiquitin stew. Science. 2002 Oct 18. PMID: 12386321
- Hochstrasser M: New structural clues to substrate specificity in the "ubiquitin system". Mol Cell. 2002 Mar. PMID: 11931752
- Laney JD, Hochstrasser M: Assaying protein ubiquitination in Saccharomyces cerevisiae. Methods Enzymol. 2002. PMID: 12073348