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First published online July 21, 2004; 10.1105/tpc.104.022236

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The Plant Cell 16:2089-2103 (2004)
© 2004 American Society of Plant Biologists

Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis

Claire Lurina, Charles Andrésa, Sébastien Aubourga, Mohammed Bellaouia, Frédérique Bittona, Clémence Bruyèreb, Michel Cabochea, Cédrig Debastc, José Gualbertod, Beate Hoffmanna, Alain Lecharnyb, Monique Le Retd, Marie-Laure Martin-Magniettea,e, Hakim Mireauc, Nemo Peetersc,1, Jean-Pierre Renoua, Boris Szureka, Ludivine Taconnata and Ian Smalla,2

a Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique/Université d'Evry Val d'Essonne), CP 5708, 91057 Evry Cedex, France
b Institut de Biotechnologie des Plantes (Centre National de la Recherche Scientifique/Université Paris-Sud), Université Paris-Sud, 91405 Orsay Cedex, France
c Station de Génétique et Amélioration des Plantes, Institut National de la Recherche Agronomique, Versailles, 78026 Versailles Cedex, France
d Institut de Biologie Moléculaire des Plantes (Centre National de la Recherche Scientifique), 67084 Strasbourg Cedex, France
e Unité Mixte de Recherche Institut National Agronomique Paris-Grignon/Ecole Nationale du Génie Rural et des Eaux et Forêts/Institut National de la Recherche Agronomique, Biométrie et Intelligence Artificielle 518, 75231 Paris, Cedex 05, France

2 To whom correspondence should be addressed. E-mail small{at}evry.inra.fr; fax 33-1-60874510.

The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.




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 J Exp BotHome page
S. Guyomarc'h, M. Benhamed, G. Lemonnier, J.-P. Renou, D.-X. Zhou, and M. Delarue
MGOUN3: evidence for chromatin-mediated regulation of FLC expression
J. Exp. Bot., June 1, 2006; 57(9): 2111 - 2119.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
M. K. Munshi, Y. Kobayashi, and T. Shikanai
CHLORORESPIRATORY REDUCTION 6 Is a Novel Factor Required for Accumulation of the Chloroplast NAD(P)H Dehydrogenase Complex in Arabidopsis
Plant Physiology, June 1, 2006; 141(2): 737 - 744.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
N. A. Eckardt
Genetic and Epigenetic Regulation of Embryogenesis
PLANT CELL, April 1, 2006; 18(4): 781 - 784.
[Full Text] [PDF]

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 Plant CellHome page
Y.-H. Ding, N.-Y. Liu, Z.-S. Tang, J. Liu, and W.-C. Yang
Arabidopsis GLUTAMINE-RICH PROTEIN23 Is Essential for Early Embryogenesis and Encodes a Novel Nuclear PPR Motif Protein That Interacts with RNA Polymerase II Subunit III
PLANT CELL, April 1, 2006; 18(4): 815 - 830.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
N. A. Eckardt
Cytoplasmic Male Sterility and Fertility Restoration
PLANT CELL, March 1, 2006; 18(3): 515 - 517.
[Full Text] [PDF]

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 Plant CellHome page
Z. Wang, Y. Zou, X. Li, Q. Zhang, L. Chen, H. Wu, D. Su, Y. Chen, J. Guo, D. Luo, et al.
Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing
PLANT CELL, March 1, 2006; 18(3): 676 - 687.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
L. Merendino, K. Perron, M. Rahire, I. Howald, J.-D. Rochaix, and M. Goldschmidt-Clermont
A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas
Nucleic Acids Res., January 10, 2006; 34(1): 262 - 274.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
J. Pfalz, K. Liere, A. Kandlbinder, K.-J. Dietz, and R. Oelmuller
pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression
PLANT CELL, January 1, 2006; 18(1): 176 - 197.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
N. Abdulrazzak, B. Pollet, J. Ehlting, K. Larsen, C. Asnaghi, S. Ronseau, C. Proux, M. Erhardt, V. Seltzer, J.-P. Renou, et al.
A coumaroyl-ester-3-hydroxylase Insertion Mutant Reveals the Existence of Nonredundant meta-Hydroxylation Pathways and Essential Roles for Phenolic Precursors in Cell Expansion and Plant Growth
Plant Physiology, January 1, 2006; 140(1): 30 - 48.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
M. Bevan and S. Walsh
The Arabidopsis genome: A foundation for plant research
Genome Res., December 1, 2005; 15(12): 1632 - 1642.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
S. Bentolila, A.-L. Chateigner-Boutin, and M. R. Hanson
Ecotype Allelic Variation in C-to-U Editing Extent of a Mitochondrial Transcript Identifies RNA-Editing Quantitative Trait Loci in Arabidopsis
Plant Physiology, December 1, 2005; 139(4): 2006 - 2016.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
A.-M. Duchene, A. Giritch, B. Hoffmann, V. Cognat, D. Lancelin, N. M. Peeters, M. Zaepfel, L. Marechal-Drouard, and I. D. Small
Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana
PNAS, November 8, 2005; 102(45): 16484 - 16489.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
B.-h. Lee, D. A. Henderson, and J.-K. Zhu
The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1
PLANT CELL, November 1, 2005; 17(11): 3155 - 3175.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
C. Vergnolle, M.-N. Vaultier, L. Taconnat, J.-P. Renou, J.-C. Kader, A. Zachowski, and E. Ruelland
The Cold-Induced Early Activation of Phospholipase C and D Pathways Determines the Response of Two Distinct Clusters of Genes in Arabidopsis Cell Suspensions
Plant Physiology, November 1, 2005; 139(3): 1217 - 1233.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
C. Schmitz-Linneweber, R. Williams-Carrier, and A. Barkan
RNA Immunoprecipitation and Microarray Analysis Show a Chloroplast Pentatricopeptide Repeat Protein to Be Associated with the 5' Region of mRNAs Whose Translation It Activates
PLANT CELL, October 1, 2005; 17(10): 2791 - 2804.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
A. C. Christensen, A. Lyznik, S. Mohammed, C. G. Elowsky, A. Elo, R. Yule, and S. A. Mackenzie
Dual-Domain, Dual-Targeting Organellar Protein Presequences in Arabidopsis Can Use Non-AUG Start Codons
PLANT CELL, October 1, 2005; 17(10): 2805 - 2816.
[Abstract] [Full Text] [PDF]

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 Genes Dev.Home page
M. Yoshikawa, A. Peragine, M. Y. Park, and R. S. Poethig
A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis
Genes & Dev., September 15, 2005; 19(18): 2164 - 2175.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
N. Juretic, D. R. Hoen, M. L. Huynh, P. M. Harrison, and T. E. Bureau
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
Genome Res., September 1, 2005; 15(9): 1292 - 1297.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
T. Czechowski, M. Stitt, T. Altmann, M. K. Udvardi, and W.-R. Scheible
Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis
Plant Physiology, September 1, 2005; 139(1): 5 - 17.
[Abstract] [Full Text] [PDF]

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 Plant CellHome page
S. Lu, Y.-H. Sun, R. Shi, C. Clark, L. Li, and V. L. Chiang
Novel and Mechanical Stress-Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsis
PLANT CELL, August 1, 2005; 17(8): 2186 - 2203.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. Murakami, K. Kuehnle, and D. B. Stern
A spontaneous tRNA suppressor of a mutation in the Chlamydomonas reinhardtii nuclear MCD1 gene required for stability of the chloroplast petD mRNA
Nucleic Acids Res., June 9, 2005; 33(10): 3372 - 3380.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
M.-L. Martin-Magniette, J. Aubert, E. Cabannes, and J.-J. Daudin
Evaluation of the gene-specific dye bias in cDNA microarray experiments
Bioinformatics, May 1, 2005; 21(9): 1995 - 2000.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
J. Allemeersch, S. Durinck, R. Vanderhaeghen, P. Alard, R. Maes, K. Seeuws, T. Bogaert, K. Coddens, K. Deschouwer, P. Van Hummelen, et al.
Benchmarking the CATMA Microarray. A Novel Tool forArabidopsis Transcriptome Analysis
Plant Physiology, February 1, 2005; 137(2): 588 - 601.
[Abstract] [Full Text] [PDF]

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 Plant Physiol.Home page
L. A. Rymarquis, J. M. Handley, M. Thomas, and D. B. Stern
Beyond Complementation. Map-Based Cloning in Chlamydomonas reinhardtii
Plant Physiology, February 1, 2005; 137(2): 557 - 566.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. Aubourg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, A. Cottet, A. Couloux, P. Dehais, G. Deleage, A. Duclert, et al.
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D641 - D646.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
D. Choury, J.-C. Farre, X. Jordana, and A. Araya
Different patterns in the recognition of editing sites in plant mitochondria
Nucleic Acids Res., December 7, 2004; 32(21): 6397 - 6406.
[Abstract] [Full Text] [PDF]


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