title: Identification of ClpP substrates in Caulobacter crescentus reveals a role for regulated proteolysis in bacterial development.
abstract: Energy-dependent proteases ensure the timely removal of unwanted proteins in a highly selective fashion. In Caulobacter crescentus, protein degradation by the ClpXP protease is critical for cell cycle progression; however, only a handful of substrates are currently known. Here, we use a trapping approach to identify putative substrates of the ClpP associated proteases in C. crescentus. Biochemical validation of several of these targets reveals specific protease recognition motifs and suggests a need for ClpXP-specific degradation beyond degradation of known cell cycle regulators. We focus on a particular instance of regulated proteolysis in Caulobacter by exploring the role of ClpXP in degrading the stalk synthesis transcription factor TacA. We show that TacA degradation is controlled during the cell cycle dependent on the ClpXP regulator CpdR and that stabilization of TacA increases degradation of another ClpXP substrate, CtrA, while restoring deficiencies associated with prolific CpdR activity. Together, our work reveals a number of new validated ClpXP substrates, clarifies rules of protease substrate selection, and demonstrates how regulated protein degradation is critical for Caulobacter development and cell cycle progression.
authors: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
authors: Nowsheen H
authors: NH
authors: Bhat
authors: Robert H
authors: RH
authors: Vass
authors: Patrick R
authors: PR
authors: Stoddard
authors: Dong K
authors: DK
authors: Shin
authors: Peter
authors: P
authors: Chien
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D016935:Caulobacter crescentus / Q000201:enzymology* / Q000378:metabolism / Q000502:physiology*; D002453:Cell Cycle; D049071:Endopeptidase Clp / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D059748:Proteolysis; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D049071:Endopeptidase Clp
references: J Mol Biol. 2002 Nov 8;323(5):785-93
references: 12417193
references: Mol Microbiol. 2006 Jan;59(2):386-401
references: 16390437
references: PLoS Biol. 2005 Oct;3(10):e334
references: 16176121
references: J Bacteriol. 2001 Sep;183(17):5001-7
references: 11489852
references: Cell. 1996 Jan 12;84(1):83-93
references: 8548829
references: Mol Cell. 2003 Mar;11(3):671-83
references: 12667450
references: J Biol Chem. 1988 Oct 15;263(29):15226-36
references: 3049606
references: Genes Dev. 2007 Feb 15;21(4):403-8
references: 17322400
references: J Bacteriol. 2008 Jan;190(1):321-31
references: 17981983
references: J Bacteriol. 2004 Sep;186(17):5856-64
references: 15317791
references: EMBO J. 1998 Oct 1;17(19):5658-69
references: 9755166
references: Genes Dev. 2008 Jan 15;22(2):212-25
references: 18198338
references: J Bacteriol. 1999 May;181(10):3039-50
references: 10322004
references: Mol Cell. 2011 Aug 19;43(4):550-60
references: 21855795
references: PLoS One. 2011 Apr 11;6(4):e18179
references: 21494595
references: Nature. 1992 Dec 10;360(6404):597-9
references: 1334232
references: Microbiol Mol Biol Rev. 2010 Mar;74(1):13-41
references: 20197497
references: Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10935-40
references: 16829582
references: Dev Cell. 2011 Mar 15;20(3):329-41
references: 21397844
references: Annu Rev Biochem. 2011;80:587-612
references: 21469952
references: J Bacteriol. 1997 Sep;179(17):5502-10
references: 9287006
references: Dev Cell. 2010 Jan 19;18(1):90-101
references: 20152180
references: Proc Natl Acad Sci U S A. 1999 Jun 8;96(12):6648-53
references: 10359766
references: Science. 2000 Dec 15;290(5499):2144-8
references: 11118148
references: J Bacteriol. 1989 Jan;171(1):392-401
references: 2536661
references: J Biol Chem. 1993 Oct 25;268(30):22618-26
references: 8226770
references: J Bacteriol. 2008 Oct;190(20):6867-80
references: 18723629
references: Nature. 2006 Dec 14;444(7121):899-904
references: 17136100
references: Structure. 2007 Oct;15(10):1296-305
references: 17937918
references: Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10614-9
references: 19541655
references: Mol Microbiol. 2005 Feb;55(4):1233-45
references: 15686567
references: Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4681-6
references: 11287652
references: Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6590-5
references: 17420450
references: J Bacteriol. 2002 Dec;184(23):6635-41
references: 12426352
references: Mol Cell. 2006 Apr 21;22(2):193-204
references: 16630889
references: Cold Spring Harb Symp Quant Biol. 2009;74:55-64
references: 19687139
references: Mol Microbiol. 2010 Mar;75(6):1539-49
references: 20158612
references: Structure. 2012 Jul 3;20(7):1223-32
references: 22682744
references: Cell. 1997 Aug 8;90(3):415-24
references: 9267022
references: Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17128-33
references: 17940001