ATP-dependent proteases of bacteria: recognition logic and operating principles

Trends in Biochemical Sciences - Tập 31 - Trang 647-653 - 2006
Tania A. Baker1,2, Robert T. Sauer1
1Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
2Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Tài liệu tham khảo

Sauer, 2004, Sculpting the proteome with AAA+ proteases and disassembly machines, Cell, 119, 9, 10.1016/j.cell.2004.09.020 Schmidt, 2005, Proteasome-associated proteins: regulation of a proteolytic machine, Biol. Chem., 386, 725, 10.1515/BC.2005.085 Ito, 2005, Cellular functions, mechanism of action, and regulation of FtsH protease, Annu. Rev. Microbiol., 59, 211, 10.1146/annurev.micro.59.030804.121316 Bukau, 2006, Molecular chaperones and protein quality control, Cell, 125, 443, 10.1016/j.cell.2006.04.014 Burton, 2005, Remodeling protein complexes: insights from the AAA+ unfoldase ClpX and Mu transposase, Protein Sci., 14, 1945, 10.1110/ps.051417505 Withey, 2003, A salvage pathway for protein structures: tmRNA and trans-translation, Annu. Rev. Microbiol., 57, 101, 10.1146/annurev.micro.57.030502.090945 Siddiqui, 2004, Role of the processing pore of the ClpX AAA+ ATPase in the recognition and engagement of specific protein substrates, Genes Dev., 18, 369, 10.1101/gad.1170304 Hinnerwisch, 2005, Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation, Cell, 121, 1029, 10.1016/j.cell.2005.04.012 Mizusawa, 1983, Protein degradation in Escherichia coli: the lon gene controls the stability of SulA protein, Proc. Natl. Acad. Sci. U. S. A., 80, 358, 10.1073/pnas.80.2.358 Gonzalez, 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, 10.1093/emboj/19.19.5251 Neher, 2006, Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon, Mol. Cell, 22, 193, 10.1016/j.molcel.2006.03.007 Neher, 2003, Latent ClpX-recognition signals ensure LexA destruction after DNA damage, Genes Dev., 17, 1084, 10.1101/gad.1078003 Flynn, 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, 10.1101/gad.1240104 Bell, 2005, Structure and mechanism of Escherichia coli RecA ATPase, Mol. Microbiol., 58, 358, 10.1111/j.1365-2958.2005.04876.x Weber-Ban, 1999, Global unfolding of a substrate protein by the Hsp100 chaperone ClpA, Nature, 401, 90, 10.1038/43481 Hoskins, 2000, Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP, Proc. Natl. Acad. Sci. U. S. A., 97, 8892, 10.1073/pnas.97.16.8892 Levchenko, 1997, ClpX and MuB interact with overlapping regions of Mu transposase: implications for control of the transposition pathway, Genes Dev., 11, 1561, 10.1101/gad.11.12.1561 Flynn, 2003, Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals, Mol. Cell, 11, 671, 10.1016/S1097-2765(03)00060-1 Ishii, 2000, Regulatory role of C-terminal residues of SulA in its degradation by Lon protease in Escherichia coli, J. Biochem. (Tokyo), 127, 837, 10.1093/oxfordjournals.jbchem.a022677 Burton, 2005, Nucleotide-dependent substrate recognition by the AAA+ HslUV protease, Nat. Struct. Mol. Biol., 12, 245, 10.1038/nsmb898 Shah, 2006, Sequence requirements for Lon-dependent degradation of the Escherichia coli transcription activator SoxS: identification of the SoxS residues critical to proteolysis and specific inhibition of in vitro degradation by a peptide comprised of the N-terminal 21 amino acid residues, J. Mol. Biol., 357, 718, 10.1016/j.jmb.2005.12.088 Hoskins, 2000, Substrate recognition by the ClpA chaperone component of ClpAP protease, J. Biol. Chem., 275, 35361, 10.1074/jbc.M006288200 Dougan, 2002, AAA+ proteins and substrate recognition, it all depends on their partner in crime, FEBS Lett., 529, 6, 10.1016/S0014-5793(02)03179-4 Levchenko, 2000, A specificity-enhancing factor for the ClpXP degradation machine, Science, 289, 2354, 10.1126/science.289.5488.2354 Wah, 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, 10.1016/S1097-2765(03)00272-7 Levchenko, 2003, Structure of a delivery protein for a AAA+ protease in complex with a peptide degradation tag, Mol. Cell, 12, 365, 10.1016/j.molcel.2003.08.014 Levchenko, 2005, Versatile modes of peptide recognition by the AAA+ adaptor protein SspB, Nat. Struct. Mol. Biol., 12, 520, 10.1038/nsmb934 McGinness, 2006, Engineering controllable protein degradation, Mol. Cell, 22, 701, 10.1016/j.molcel.2006.04.027 Prakash, 2004, An unstructured initiation site is required for efficient proteasome-mediated degradation, Nat. Struct. Mol. Biol., 11, 830, 10.1038/nsmb814 Dougan, 2002, ClpS, a substrate modulator of the ClpAP machine, Mol. Cell, 9, 673, 10.1016/S1097-2765(02)00485-9 Erbse, 2006, ClpS is an essential component of the N-end rule pathway in Escherichia coli, Nature, 439, 753, 10.1038/nature04412 Hilliard, 1998, PinA inhibits ATP hydrolysis and energy-dependent protein degradation by Lon protease, J. Biol. Chem., 273, 524, 10.1074/jbc.273.1.524 Flynn, 2001, Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis, Proc. Natl. Acad. Sci. U. S. A., 98, 10584, 10.1073/pnas.191375298 Neher, 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. U. S. A., 100, 13219, 10.1073/pnas.2235804100 Kim, 2000, Dynamics of substrate denaturation and translocation by the ClpXP degradation machine, Mol. Cell, 5, 639, 10.1016/S1097-2765(00)80243-9 Lee, 2001, ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal, Mol. Cell, 7, 627, 10.1016/S1097-2765(01)00209-X Kenniston, 2003, Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine, Cell, 114, 511, 10.1016/S0092-8674(03)00612-3 Kenniston, 2004, Effects of local protein stability and the geometric position of the substrate degradation tag on the efficiency of ClpXP denaturation and degradation, J. Struct. Biol., 146, 130, 10.1016/j.jsb.2003.10.023 Martin, 2005, Rebuilt AAA+ motors reveal operating principles for ATP-fueled machines, Nature, 437, 1115, 10.1038/nature04031 Kenniston, 2005, Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing, Proc. Natl. Acad. Sci. U. S. A., 102, 1390, 10.1073/pnas.0409634102 Yamada-Inagawa, 2003, Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis, J. Biol. Chem., 278, 50182, 10.1074/jbc.M308327200 Park, 2005, Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase, J. Biol. Chem., 280, 22892, 10.1074/jbc.M500035200 Bochtler, 2000, The structures of HsIU and the ATP-dependent protease HsIU–HsIV, Nature, 403, 800, 10.1038/35001629 Sousa, 2000, Crystal and solution structures of an HslUV protease-chaperone complex, Cell, 103, 633, 10.1016/S0092-8674(00)00166-5 Wang, 2001, Nucleotide-dependent conformational changes in a protease-associated ATPase HslU, Structure, 9, 1107, 10.1016/S0969-2126(01)00670-0 Hersch, 2005, Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine, Cell, 121, 1017, 10.1016/j.cell.2005.05.024