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J. Biol. Chem., Vol. 278, Issue 36, 33774-33785, September 5, 2003

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Proteomic Characterization of the Chlamydomonas reinhardtii Chloroplast Ribosome

IDENTIFICATION OF PROTEINS UNIQUE TO THE 70 S RIBOSOME^*,

Kenichi Yamaguchi  , María Verónica Beligni , Susana Prieto  ¶, Paul A. Haynes ||, W. Hayes McDonald **, John R. Yates, III ** and Stephen P. Mayfield  

From the Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, the ^||Torrey Mesa Research Institute of Syngenta, San Diego, California 92121, and the ^**Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037

We have conducted a proteomic analysis of the 70 S ribosome from the Chlamydomonas reinhardtii chloroplast. Twenty-seven orthologs of Escherichia coli large subunit proteins were identified in the 50 S subunit, as well as an ortholog of the spinach plastid-specific ribosomal protein-6. Several of the large subunit proteins of C. reinhardtii have short extension or insertion sequences, but overall the large subunit proteins are very similar to those of spinach chloroplast and E. coli. Two proteins of 38 and 41 kDa, designated RAP38 and RAP41, were identified from the 70 S ribosome that were not found in either of the ribosomal subunits. Phylogenetic analysis identified RAP38 and RAP41 as paralogs of spinach CSP41, a chloroplast RNA-binding protein with endoribonuclease activity. Overall, the chloroplast ribosome of C. reinhardtii is similar to those of spinach chloroplast and E. coli, but the C. reinhardtii ribosome has proteins associated with the 70 S complex that are related to non-ribosomal proteins in other species. In addition, the 30 S subunit contains unusually large orthologs of E. coli S2, S3, and S5 and a novel S1-type protein (Yamaguchi, K. et al., (2002) Plant Cell 14, 2957–2974). These additional proteins and domains likely confer functions used to regulate chloroplast translation in C. reinhardtii.

Received for publication, February 24, 2003 , and in revised form, June 9, 2003.

The nucleic acid sequences reported in this paper have been submitted to the GenBank^TM/EMBL Data Bank with accession numbers AY177617 (Rap38) and AY177616 (Rap41).

^* This work was supported by Grant GM54659 from the National Institutes of Health, Contract DE-FG03-93ER70116 from the Department of Energy, and a grant from Syngenta Corp. (all to S. P. M.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains a supplementary figure.

Supported by a Skaggs postdoctoral fellowship. Present address: Division of Biochemistry, Faculty of Fisheries, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521, Japan.

^¶ Present address: Centre de Recherche de Biochimie Macromoleculaire (CRBM), CNRS UPR 1086, 34293 Montpellier Cedex 5, France.

To whom correspondence should be addressed: Dept. of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-9848; Fax: 858-784-9840; E-mail: mayfield{at}scripps.edu.

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