Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis

Plant Cell. 2006 Jul;18(7):1704-21. doi: 10.1105/tpc.106.042861. Epub 2006 Jun 9.


Plastids contain tetradecameric Clp protease core complexes, with five ClpP Ser-type proteases, four nonproteolytic ClpR, and two associated ClpS proteins. Accumulation of total ClpPRS complex decreased twofold to threefold in an Arabidopsis thaliana T-DNA insertion mutant in CLPR2 designated clpr2-1. Differential stable isotope labeling of the ClpPRS complex with iTRAQ revealed a fivefold reduction in assembled ClpR2 accumulation and twofold to fivefold reductions in the other subunits. A ClpR2:(his)(6) fusion protein that incorporated into the chloroplast ClpPRS complex fully complemented clpr2-1. The reduced accumulation of the ClpPRS protease complex led to a pale-green phenotype with delayed shoot development, smaller chloroplasts, decreased thylakoid accumulation, and increased plastoglobule accumulation. Stromal ClpC1 and 2 were both recruited to the thylakoid surface in clpr2-1. The thylakoid membrane of clpr2-1 showed increased carotenoid content, partial inactivation of photosystem II, and upregulated thylakoid proteases and stromal chaperones, suggesting an imbalance in chloroplast protein homeostasis and a well-coordinated network of proteolysis and chaperone activities. Interestingly, a subpopulation of PsaF and several light-harvesting complex II proteins accumulated in the thylakoid with unprocessed chloroplast transit peptides. We conclude that ClpR2 cannot be functionally replaced by other ClpP/R homologues and that the ClpPRS complex is central to chloroplast biogenesis, thylakoid protein homeostasis, and plant development.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Arabidopsis* / cytology
  • Arabidopsis* / enzymology
  • Arabidopsis* / physiology
  • Chloroplasts / metabolism*
  • Chloroplasts / ultrastructure
  • Down-Regulation
  • Electron Transport Chain Complex Proteins / genetics
  • Electron Transport Chain Complex Proteins / metabolism
  • Endopeptidase Clp / genetics
  • Endopeptidase Clp / metabolism*
  • Gene Expression Regulation, Enzymologic*
  • Gene Expression Regulation, Plant*
  • Homeostasis
  • Molecular Chaperones / metabolism
  • Molecular Sequence Data
  • Multienzyme Complexes
  • Phenotype
  • Photoperiod
  • Photosystem II Protein Complex / physiology
  • Pigments, Biological / metabolism
  • Plant Leaves / metabolism
  • Plant Leaves / ultrastructure
  • Plants, Genetically Modified
  • Plastids / enzymology
  • Sequence Alignment
  • Starch / metabolism
  • Thylakoids / chemistry
  • Thylakoids / metabolism
  • Thylakoids / ultrastructure


  • Arabidopsis Proteins
  • Electron Transport Chain Complex Proteins
  • Molecular Chaperones
  • Multienzyme Complexes
  • Photosystem II Protein Complex
  • Pigments, Biological
  • Starch
  • Endopeptidase Clp