ClpP

• Description: ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein)
  
  

Gene name	clpP
Synonyms	yvdN
Essential	no
Product	ATP-dependent Clp protease proteolytic subunit
Function	protein degradation
Interactions involving this protein in SubtInteract: ClpP
Metabolic function and regulation of this protein in SubtiPathways: Phosphorelay, Stress
MW, pI	21 kDa, 5.008
Gene length, protein length	591 bp, 197 aa
Immediate neighbours	trnQ-Arg, pgcM
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

Categories containing this gene/protein

proteolysis, general stress proteins (controlled by SigB), heat shock proteins

This gene is a member of the following regulons

CtsR regulon, SigB regulon

The gene

Basic information

• Locus tag: BSU34540

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot) endopeptidase/proteolysis

• Protein family: peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) InterPro, (PF00574) PFAM

• Paralogous protein(s):

Targets of ClpC-ClpP-dependent protein degradation

• DegU-P PubMed

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:
  • the novel antibiotic ADEP (acyldepsipeptides) dysregulates ClpP activity and allows FtsZ degradation in the absence of an ATPase subunit (ClpC, ClpE, or ClpX) PubMed

• Interactions:
  • ClpE-ClpP, ClpC-ClpP, ClpX-ClpP
  • CtsR-ClpP/ClpC (degradation of CtsR) PubMed
  • McsB-ClpP/ClpC (rapid degradation of non-phosphorylated McsB) PubMed
  • Spx-ClpP/ClpX (degradation of Spx) PubMed

• Localization:
  • cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heat shock, colocalization with ClpX, ClpC and ClpE PubMed

Database entries

• Structure: 3KTG PubMed

• UniProt: P80244

• KEGG entry: [3]

• E.C. number: 3.4.21.92

Expression and regulation

• Operon: clpP PubMed

• Sigma factor: SigA PubMed, SigB PubMed

• Regulation:
  • induced by stress (SigB) PubMed
  • induced by heat (CtsR) PubMed

• Regulatory mechanism:
  • CtsR: transcription repression PubMed

• Additional information:

Biological materials

• Mutant:
  • clpP::spec and clpP::cat, available in the Leendert Hamoen lab
  • GP551 (spc), available in the Stülke lab

• Expression vector:

• lacZ fusion:

• GFP fusion: C-terminal GFP fusions (both single copy and as 2th copy in amyE locus, also as CFP and YFP variants) available in the Leendert Hamoen lab

• two-hybrid system:

• Antibody:

Labs working on this gene/protein

Leendert Hamoen, Newcastle University, UK homepage

References

Reviews

Additional reviews: PubMed

Dorte Frees, Kirsi Savijoki, Pekka Varmanen, Hanne Ingmer
Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria.
Mol Microbiol: 2007, 63(5);1285-95
[PubMed:17302811] [WorldCat.org] [DOI] (P p)

John S Blanchard
Old approach yields new antibiotic.
Nat Med: 2005, 11(10);1045-6
[PubMed:16211032] [WorldCat.org] [DOI] (P p)

Original Publications

Additional publications: PubMed

Byung-Gil Lee, Min Kyung Kim, Hyun Kyu Song
Structural insights into the conformational diversity of ClpP from Bacillus subtilis.
Mol Cells: 2011, 32(6);589-95
[PubMed:22080375] [WorldCat.org] [DOI] (I p)

Peter Sass, Michaele Josten, Kirsten Famulla, Guido Schiffer, Hans-Georg Sahl, Leendert Hamoen, Heike Brötz-Oesterhelt
Antibiotic acyldepsipeptides activate ClpP peptidase to degrade the cell division protein FtsZ.
Proc Natl Acad Sci U S A: 2011, 108(42);17474-9
[PubMed:21969594] [WorldCat.org] [DOI] (I p)

Alexander K W Elsholz, Stephan Michalik, Daniela Zühlke, Michael Hecker, Ulf Gerth
CtsR, the Gram-positive master regulator of protein quality control, feels the heat.
EMBO J: 2010, 29(21);3621-9
[PubMed:20852588] [WorldCat.org] [DOI] (I p)

Byung-Gil Lee, Eun Young Park, Kyung-Eun Lee, Hyesung Jeon, Kwang Hoon Sung, Holger Paulsen, Helga Rübsamen-Schaeff, Heike Brötz-Oesterhelt, Hyun Kyu Song
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
Nat Struct Mol Biol: 2010, 17(4);471-8
[PubMed:20305655] [WorldCat.org] [DOI] (I p)

Mitsuo Ogura, Kensuke Tsukahara
Autoregulation of the Bacillus subtilis response regulator gene degU is coupled with the proteolysis of DegU-P by ClpCP.
Mol Microbiol: 2010, 75(5);1244-59
[PubMed:20070525] [WorldCat.org] [DOI] (I p)

Ziqing Mei, Feng Wang, Yutao Qi, Zhiyuan Zhou, Qi Hu, Han Li, Jiawei Wu, Yigong Shi
Molecular determinants of MecA as a degradation tag for the ClpCP protease.
J Biol Chem: 2009, 284(49);34366-75
[PubMed:19767395] [WorldCat.org] [DOI] (I p)

Jeanette Hahn, Naomi Kramer, Kenneth Briley, David Dubnau
McsA and B mediate the delocalization of competence proteins from the cell poles of Bacillus subtilis.
Mol Microbiol: 2009, 72(1);202-15
[PubMed:19226326] [WorldCat.org] [DOI] (I p)

James Kain, Gina G He, Richard Losick
Polar localization and compartmentalization of ClpP proteases during growth and sporulation in Bacillus subtilis.
J Bacteriol: 2008, 190(20);6749-57
[PubMed:18689476] [WorldCat.org] [DOI] (I p)

Lyle A Simmons, Alan D Grossman, Graham C Walker
Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis.
J Bacteriol: 2008, 190(20);6758-68
[PubMed:18689473] [WorldCat.org] [DOI] (I p)

Adam Reeves, Ulf Gerth, Uwe Völker, W G Haldenwang
ClpP modulates the activity of the Bacillus subtilis stress response transcription factor, sigmaB.
J Bacteriol: 2007, 189(17);6168-75
[PubMed:17586624] [WorldCat.org] [DOI] (P p)

Peter Prepiak, David Dubnau
A peptide signal for adapter protein-mediated degradation by the AAA+ protease ClpCP.
Mol Cell: 2007, 26(5);639-47
[PubMed:17560370] [WorldCat.org] [DOI] (P p)

Stephan Zellmeier, Wolfgang Schumann, Thomas Wiegert
Involvement of Clp protease activity in modulating the Bacillus subtilissigmaw stress response.
Mol Microbiol: 2006, 61(6);1569-82
[PubMed:16899079] [WorldCat.org] [DOI] (P p)

Heike Brötz-Oesterhelt, Dieter Beyer, Hein-Peter Kroll, Rainer Endermann, Christoph Ladel, Werner Schroeder, Berthold Hinzen, Siegfried Raddatz, Holger Paulsen, Kerstin Henninger, Julia E Bandow, Hans-Georg Sahl, Harald Labischinski
Dysregulation of bacterial proteolytic machinery by a new class of antibiotics.
Nat Med: 2005, 11(10);1082-7
[PubMed:16200071] [WorldCat.org] [DOI] (P p)

Holger Kock, Ulf Gerth, Michael Hecker
The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis.
J Bacteriol: 2004, 186(17);5856-64
[PubMed:15317791] [WorldCat.org] [DOI] (P p)

Holger Kock, Ulf Gerth, Michael Hecker
MurAA, catalysing the first committed step in peptidoglycan biosynthesis, is a target of Clp-dependent proteolysis in Bacillus subtilis.
Mol Microbiol: 2004, 51(4);1087-102
[PubMed:14763982] [WorldCat.org] [DOI] (P p)

Ulf Gerth, Janine Kirstein, Jörg Mostertz, Torsten Waldminghaus, Marcus Miethke, Holger Kock, Michael Hecker
Fine-tuning in regulation of Clp protein content in Bacillus subtilis.
J Bacteriol: 2004, 186(1);179-91
[PubMed:14679237] [WorldCat.org] [DOI] (P p)

Qi Pan, Richard Losick
Unique degradation signal for ClpCP in Bacillus subtilis.
J Bacteriol: 2003, 185(17);5275-8
[PubMed:12923101] [WorldCat.org] [DOI] (P p)

Tiina Pummi, Soile Leskelä, Eva Wahlström, Ulf Gerth, Harold Tjalsma, Michael Hecker, Matti Sarvas, Vesa P Kontinen
ClpXP protease regulates the signal peptide cleavage of secretory preproteins in Bacillus subtilis with a mechanism distinct from that of the Ecs ABC transporter.
J Bacteriol: 2002, 184(4);1010-8
[PubMed:11807061] [WorldCat.org] [DOI] (P p)

Q Pan, D A Garsin, R Losick
Self-reinforcing activation of a cell-specific transcription factor by proteolysis of an anti-sigma factor in B. subtilis.
Mol Cell: 2001, 8(4);873-83
[PubMed:11684022] [WorldCat.org] [DOI] (P p)

A Petersohn, M Brigulla, S Haas, J D Hoheisel, U Völker, M Hecker
Global analysis of the general stress response of Bacillus subtilis.
J Bacteriol: 2001, 183(19);5617-31
[PubMed:11544224] [WorldCat.org] [DOI] (P p)

H Nanamiya, K Takahashi, M Fujita, F Kawamura
Deficiency of the initiation events of sporulation in Bacillus subtilis clpP mutant can be suppressed by a lack of the Spo0E protein phosphatase.
Biochem Biophys Res Commun: 2000, 279(1);229-33
[PubMed:11112444] [WorldCat.org] [DOI] (P p)

E Krüger, E Witt, S Ohlmeier, R Hanschke, M Hecker
The clp proteases of Bacillus subtilis are directly involved in degradation of misfolded proteins.
J Bacteriol: 2000, 182(11);3259-65
[PubMed:10809708] [WorldCat.org] [DOI] (P p)

I Derré, G Rapoport, T Msadek
CtsR, a novel regulator of stress and heat shock response, controls clp and molecular chaperone gene expression in gram-positive bacteria.
Mol Microbiol: 1999, 31(1);117-31
[PubMed:9987115] [WorldCat.org] [DOI] (P p)

U Gerth, E Krüger, I Derré, T Msadek, M Hecker
Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance.
Mol Microbiol: 1998, 28(4);787-802
[PubMed:9643546] [WorldCat.org] [DOI] (P p)

T Msadek, V Dartois, F Kunst, M L Herbaud, F Denizot, G Rapoport
ClpP of Bacillus subtilis is required for competence development, motility, degradative enzyme synthesis, growth at high temperature and sporulation.
Mol Microbiol: 1998, 27(5);899-914
[PubMed:9535081] [WorldCat.org] [DOI] (P p)