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J. Biol. Chem., Vol. 276, Issue 19, 16318-16327, May 11, 2001
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From the A 350-kDa ClpP protease complex with 10 different
subunits was identified in chloroplast of Arabidopsis
thaliana, using Blue-Native gel electrophoresis, followed by
matrix-assisted laser desorption ionization time-of-flight and
nano-electrospray tandem mass spectrometry. The complex was copurified
with the thylakoid membranes, and all identified Clp subunits show
chloroplast targeting signals, supporting that this complex is indeed
localized in the chloroplast. The complex contains chloroplast-encoded
pClpP and six nuclear-encoded proteins nCpP1-6, as well as two
unassigned Clp homologues (nClpP7, nClpP8). An additional Clp protein
was identified in this complex; it does not belong to any of the known
Clp genes families and is here assigned ClpS1. Expression and
accumulation of several of these Clp proteins have never been shown
earlier. Sequence and phylogenetic tree analysis suggests that nClpP5,
nClpP2, and nClpP8 are not catalytically active and form a new group of
Clp higher plant proteins, orthologous to the cyanobacterial ClpR protein, and are renamed ClpR1, -2, and -3, respectively. We speculate that ClpR1, -2, and -3 are part of the heptameric rings, whereas ClpS1
is a regulatory subunit positioned at the axial opening of the ClpP/R
core. Several truncations and errors in intron and exon prediction of
the annotated Clp genes were corrected using mass spectrometry data and
by matching genomic sequences with cDNA sequences. This strategy
will be widely applicable for the much needed verification of protein
prediction from genomic sequence. The extreme complexity of the
chloroplast Clp complex is discussed.
Identification of a 350-kDa ClpP Protease Complex with 10 Different Clp Isoforms in Chloroplasts of Arabidopsis
thaliana*
§,§¶,
,, and§§
Department of Biochemistry, Arrhenius
Laboratories, Stockholm University, S-10691 Stockholm, Sweden, the
Stockholm Bioinformatics Center, Stockholm University, S-10691
Stockholm, Sweden, and the ** Department of Molecular Biology, Odense
University, DK-5230 Odense M, Denmark
*
This work was supported in part by the Swedish Agricultural
Research Council, the Swedish Foundation Strategic Research, a grant
for two-dimensional equipment from the Swedish National Research
Council, and a grant for mass spectrometers from the Hasselblad
Foundation (to K. J. v. W.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
Member of the Center for Experimental Bioinformatics sponsored
by the Danish National Research Foundation.
§§
To whom correspondence should be addressed. Present address:
Dept. of Plant Biology, Emerson Bldg., 3rd Fl., Tower Rd., Cornell University, Ithaca, NY 14853. Tel.: 607-254-1211; Fax:
607-255-5407; E-mail: kv35@cornell.edu.
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