Engineering Controllable Protein Degradation

Molecular Cell

Volumn 22, Issue 5, 2006, Pages 701-707

  McGinness, Kathleen E ^a   Baker, Tania A ^a   Sauer, Robert T ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

PROTEINS

Indexed keywords

PROTEINASE;

ARTICLE; CONTROLLED STUDY; CYTOSOL; ESCHERICHIA COLI; GENE SEQUENCE; NONHUMAN; PROTEIN DEGRADATION; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FUNCTION;

AMINO ACID SEQUENCE; CARRIER PROTEINS; CYTOSOL; ENDOPEPTIDASE CLP; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PROTEIN ENGINEERING; SUBSTRATE SPECIFICITY;

EID: 33744518327     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2006.04.027     Document Type: Article

References (29)

1. Bolon D.N., Grant R.A., Baker T.A., and Sauer R.T. Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease. Mol. Cell 16 (2004) 343-350
2. Burton B.M., Williams T.L., and Baker T.A. ClpX-mediated remodeling of mu transpososomes: selective unfolding of subunits destabilizes the entire complex. Mol. Cell 8 (2001) 449-454
3. Burton R.E., Siddiqui S.M., Kim Y.I., Baker T.A., and Sauer R.T. Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine. EMBO J. 20 (2001) 3092-3100
4. Chivers P.T., and Sauer R.T. NikR is a ribbon-helix-helix DNA-binding protein. Protein Sci. 8 (1999) 2494-2500
5. Farrell C.M., Grossman A.D., and Sauer R.T. Cytoplasmic degradation of ssrA-tagged proteins. Mol. Microbiol. 57 (2005) 1750-1761
6. Flynn J.M., Levchenko I., Seidel M., Wickner S.H., Sauer R.T., and Baker T.A. Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc. Natl. Acad. Sci. USA 98 (2001) 10584-10589
7. Flynn J.M., Neher S.B., Kim Y.I., Sauer R.T., and Baker T.A. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol. Cell 11 (2003) 671-683
8. Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., and Weissman J.S. Global analysis of protein expression in yeast. Nature 425 (2003) 737-741
9. Gottesman S., Roche E., Zhou Y., and Sauer R.T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12 (1998) 1338-1347
10. Hayes C.S., and Sauer R.T. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12 (2003) 903-911
11. Herman C., Thevenet D., Bouloc P., Walker G.C., and D'Ari R. Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev. 12 (1998) 1348-1355
12. Herring C.D., and Blattner F.R. Conditional lethal amber mutations in essential Escherichia coli genes. J. Bacteriol. 186 (2004) 2673-2681
13. Hersch G.L., Baker T.A., and Sauer R.T. SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc. Natl. Acad. Sci. USA 101 (2004) 12136-12141
14. 6 unfoldase: allosteric control of a protein machine. Cell 121 (2005) 1017-1027
15. Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., and O'Shea E.K. Global analysis of protein localization in budding yeast. Nature 425 (2003) 686-691
16. Janse D.M., Crosas B., Finley D., and Church G.M. Localization to the proteasome is sufficient for degradation. J. Biol. Chem. 279 (2004) 21415-21420
17. Kenniston J.A., Baker T.A., Fernandez J.M., and Sauer R.T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114 (2003) 511-520
18. Kim Y.I., Burton R.E., Burton B.M., Sauer R.T., and Baker T.A. Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol. Cell 5 (2000) 639-648
19. Lee C., Schwartz M.P., Prakash S., Iwakura M., and Matouschek A. ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol. Cell 7 (2001) 627-637
20. Levchenko I., Seidel M., Sauer R.T., and Baker T.A. A specificity-enhancing factor for the ClpXP degradation machine. Science 289 (2000) 2354-2356
21. Matsuzawa S., Cuddy M., Fukushima T., and Reed J.C. Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway. Proc. Natl. Acad. Sci. USA 102 (2005) 14982-14987
22. Neher S.B., Sauer R.T., and Baker T.A. Distinct peptide signals in the UmuD and UmuD′ subunits of UmuD/D′ mediate tethering and substrate processing by the ClpXP protease. Proc. Natl. Acad. Sci. USA 100 (2003) 13219-13224
23. Pruteanu M., and Hengge-Aronis R. The cellular level of the recognition factor RssB is rate-limiting for sigmaS proteolysis: implications for RssB regulation and signal transduction in sigmaS turnover in Escherichia coli. Mol. Microbiol. 45 (2002) 1701-1713
24. + proteases and disassembly machines. Cell 119 (2004) 9-18
25. Vershon A.K., Blackmer K., and Sauer R.T. Mutagenesis of the Arc repressor using synthetic primers with random nucleotide substitutions. In: Inouye M., and Sarma R. (Eds). Protein Engineering: Applications in Science, Medicine, and Industry (1986), Academic Press, Orlando, Florida 243-256
26. Wah D.A., Levchenko I., Rieckhof G.E., Bolon D.N., Baker T.A., and Sauer R.T. Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. Mol. Cell 12 (2003) 355-363
27. Zhang X., and Bremer H. Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J. Biol. Chem. 270 (1995) 11181-11189
28. Zhou P. Targeted protein degradation. Curr. Opin. Chem. Biol. 9 (2005) 51-55
29. Zhou Y., Gottesman S., Hoskins J.R., Maurizi M.R., and Wickner S. The RssB response regulator directly targets sigma(S) for degradation by ClpXP. Genes Dev. 15 (2001) 627-637