Article
You have full text access to this OnlineOpen article
Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species
Article first published online: 10 DEC 2009
DOI: 10.1002/pro.306
Copyright © 2010 The Protein Society
Additional Information
How to Cite
Chowdhury, T., Chien, P., Ebrahim, S., Sauer, R. T. and Baker, T. A. (2010), Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Science, 19: 242–254. doi: 10.1002/pro.306
Publication History
- Issue published online: 21 JAN 2010
- Article first published online: 10 DEC 2009
- Accepted manuscript online: 10 DEC 2009 12:00AM EST
- Manuscript Accepted: 30 NOV 2009
- Manuscript Received: 18 SEP 2009
Funded by
- NIH. Grant Numbers: GM49224, AI16892, 5K99GM084157
References
- 1( 2003) Proteolysis in bacterial regulatory circuits. Annu Rev Cell Dev Biol 19: 565–587.
- 2, , , , , , ( 2002) Functional proteolytic complexes of the human mitochondrial ATP-dependent protease, hClpXP. J Biol Chem 277: 21095–21102.
- 3, ( 1998) An essential protease involved in bacterial cell-cycle control. Embo J 17: 5658–5669.
- 4, , , ( 1998) Mcx1p, a ClpX homologue in mitochondria of Saccharomyces cerevisiae. FEBS Lett 438: 250–254.
- 5, , ( 1997) The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis. Cell 91: 447–456.
- 6, , ( 1996) Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271: 990–993.
- 7, , , ( 1998) The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev 12: 1338–1347.
- 8, , , ( 2000) A specificity-enhancing factor for the ClpXP degradation machine. Science 289: 2354–2356.
- 9, , , , ( 2001) The RssB response regulator directly targets sigma(S) for degradation by ClpXP. Genes Dev 15: 627–637.
- 10, , ( 2003) 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: 13219–13224.
- 11, , , ( 2004) Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation. Genes Dev 18: 2292–2301.
- 12, , , ( 2003) The N-terminal zinc binding domain of ClpX is a dimerization domain that modulates the chaperone function. J Biol Chem 278: 48981–48990.
- 13, , ( 2003) Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J Biol Chem 278: 48991–48996.
- 14, , , , , , ( 2001) Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J Biol Chem 276: 29420–29429.
- 15, , ( 2003) Targeted delivery of an ssrA-tagged substrate by the adaptor protein SspB to its cognate AAA+ protein ClpX. Mol Cell 12: 373–380.
- 16, , , , , , ( 2006) Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX. Proc Natl Acad Sci USA 103: 17724–17729.
- 17, , , ( 2007) Structure and substrate specificity of an SspB ortholog: design implications for AAA+ adaptors. Structure 15: 1296–1305.
- 18, , , ( 2008) Unique contacts direct high-priority recognition of the tetrameric Mu transposase-DNA complex by the AAA+ unfoldase ClpX. Mol Cell 30: 39–50.
- 19, , , , ( 2003) Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol Cell 12: 365–372.
- 20, ( 2003) Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine. Mol Cell 12: 75–86.
- 21, , , , , ( 2003) 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: 355–363.
- 22, , , , ( 2004) Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Mol Cell 13: 443–449.
- 23, , , , , ( 2007) Structural basis of SspB-tail recognition by the zinc binding domain of ClpX. J Mol Biol 367: 514–526.
- 24, , , ( 2002) Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer. Chem Biol 9: 1237–1245.
- 25, , , , ( 2007) Direct and adaptor-mediated substrate recognition by an essential AAA+ protease. Proc Natl Acad Sci USA 104: 6590–6595.
- 26, , ( 2007) Proteolytic adaptor for transfer-messenger RNA-tagged proteins from alpha-proteobacteria. J Bacteriol 189: 272–275.
- 27, , , ( 2004) Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease. Mol Cell 16: 343–350.
- 28, , , ( 2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190.
- 29, , , ( 2004) The Jalview Java alignment editor. Bioinformatics 20: 426–427.
- 30, , ( 2006) Engineering controllable protein degradation. Mol Cell 22: 701–707.
- 31, , , , ( 2007) Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J Biol Chem 282: 11465–11473.
- 32( 2009) Mechanistic Studies of the AAA+ Motor Protein ClpXP. Ph.D Thesis, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
- 33, , , , , ( 2001) Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc Natl Acad Sci USA 98: 10584–10589.
- 34, , , ( 2000) Subunit-specific degradation of the UmuD/D' heterodimer by the ClpXP protease: the role of trans recognition in UmuD' stability. Embo J 19: 5251–5258.
- 35, , , , ( 1997) PDZ-like domains mediate binding specificity in the Clp/Hsp100 family of chaperones and protease regulatory subunits. Cell 91: 939–947.
- 36, , , , ( 2005) Versatile modes of peptide recognition by the AAA+ adaptor protein SspB. Nat Struct Mol Biol 12: 520–525.
- 37, , , , ( 2003) Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell 11: 671–683.
- 38, , , ( 1998) Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis. Genes Dev 12: 3889–3899.
- 39, , ( 2000) Substrate recognition by the ClpA chaperone component of ClpAP protease. J Biol Chem 275: 35361–35367.
- 40, ( 2001) Regulation of SulA cleavage by Lon protease by the C-terminal amino acid of SulA, histidine. Biochem J 358: 473–480.
- 41, , . ( 2004) Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons. Mol Microbiol 51: 1801–1816.Direct Link:
- 42, ( 2006) Two peptide sequences can function cooperatively to facilitate binding and unfolding by ClpA and degradation by ClpAP. Proc Natl Acad Sci USA 103: 909–914.
- 43, , , , , , , ( 2006) ClpS is an essential component of the N-end rule pathway in Escherichia coli. Nature 439: 753–756.
- 44, , ( 2007) ClpS modulates but is not essential for bacterial N-end rule degradation. Genes Dev 21: 403–408.
- 45, ( 2008) Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev 22: 2267–2277.
- 46, , , , , , ( 2008) Insights into adaptor binding to the AAA protein p97. Biochem Soc Trans 36: 62–67.
- 47, ( 2006) ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci 31: 647–653.
- 48, , , ( 1998) Green fluorescent protein purification by organic extraction. Protein Expr Purif 14: 382–386.
- 49, , , , ( 2000) Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol Cell 5: 639–648.
- 50, , , , ( 2005) Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol 3: 1770–1788.

1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
