|
Plant Physiol, October 2001, Vol. 127, pp. 398-415
The Organization of Cytoplasmic Ribosomal Protein Genes in the
Arabidopsis Genome1
Abdelali
Barakat,2
Kathleen
Szick-Miranda,2
Ing-Feng
Chang,
Romain
Guyot,
Guillaume
Blanc,
Richard
Cooke,
Michel
Delseny,3 and
Julia
Bailey-Serres3*
Laboratoire Génome et Développement des Plantes,
Unité Mixte de Recherche 5096 Centre National de la Recherche
Scientifique, Université de Perpignan, 52, Avenue de
Villeneuve, 66860 Perpignan cedex, France (A.B., R.G., G.B., R.C.,
M.D.); and Department of Botany and Plant Sciences, University of
California, Riverside, California 92521-0124 (K.S.-M., I.-F.C,
J.B.-S.)
Eukaryotic ribosomes are made of two components, four ribosomal
RNAs, and approximately 80 ribosomal proteins (r-proteins). The exact
number of r-proteins and r-protein genes in higher plants is not known.
The strong conservation in eukaryotic r-protein primary sequence
allowed us to use the well-characterized rat (Rattus
norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of Arabidopsis. By use of the numerous expressed sequence tag (EST) accessions and the complete genomic sequence of this species, we identified 249 genes (including some pseudogenes) corresponding to 80 (32 small subunit and 48 large subunit) cytoplasmic r-protein types. None of the r-protein genes are
single copy and most are encoded by three or four expressed genes,
indicative of the internal duplication of the Arabidopsis genome. The
r-proteins are distributed throughout the genome. Inspection of genes
in the vicinity of r-protein gene family members confirms extensive
duplications of large chromosome fragments and sheds light on the
evolutionary history of the Arabidopsis genome. Examination of large
duplicated regions indicated that a significant fraction of the
r-protein genes have been either lost from one of the duplicated
fragments or inserted after the initial duplication event. Only 52 r-protein genes lack a matching EST accession, and 19 of these contain
incomplete open reading frames, confirming that most genes are
expressed. Assessment of cognate EST numbers suggests that r-protein
gene family members are differentially expressed.
1
This work was supported by the European Union
EudicotMap program (contract no. BIO 4CT 97-2170); by the Centre
National de la Recherche Scientifique and the French Ministry
of National Education, Research, and Technology (grants to M.D.); and
by the U.S. Department of Agriculture/National Research
Initiative Competitive Grants Program (grant no.
00-35301-9108 to J.B.-S.).
2
These authors contributed equally to the paper.
3
These laboratories contributed equally to the paper.
*
Corresponding author; e-mail serres{at}mail.ucr.edu; fax
909- 787-4437.
© 2001 American Society of Plant Physiologists
This article has been cited by other articles:
|
|
|
|
 
R. F. Degenhardt and P. C. Bonham-Smith
Arabidopsis Ribosomal Proteins RPL23aA and RPL23aB Are Differentially Targeted to the Nucleolus and Are Disparately Required for Normal Development
Plant Physiology,
May 1, 2008;
147(1):
128 - 142.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
V. Pinon, J. P. Etchells, P. Rossignol, S. A. Collier, J. M. Arroyo, R. A. Martienssen, and M. E. Byrne
Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins
Development,
April 1, 2008;
135(7):
1315 - 1324.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. J. Carroll, J. L. Heazlewood, J. Ito, and A. H. Millar
Analysis of the Arabidopsis Cytosolic Ribosome Proteome Provides Detailed Insights into Its Components and Their Post-translational Modification
Mol. Cell. Proteomics,
February 1, 2008;
7(2):
347 - 369.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. R. Schulze, B. F. McAllister, D. A. R. Sinclair, K. A. Fitzpatrick, M. Marchetti, S. Pimpinelli, and B. M. Honda
Heterochromatic Genes in Drosophila: A Comparative Analysis of Two Genes
Genetics,
July 1, 2006;
173(3):
1433 - 1445.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. Hirsch, V. Lefort, M. Vankersschaver, A. Boualem, A. Lucas, C. Thermes, Y. d'Aubenton-Carafa, and M. Crespi
Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts
Plant Physiology,
April 1, 2006;
140(4):
1192 - 1204.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Casasoli, J. Derory, C. Morera-Dutrey, O. Brendel, I. Porth, J.-M. Guehl, F. Villani, and A. Kremer
Comparison of Quantitative Trait Loci for Adaptive Traits Between Oak and Chestnut Based on an Expressed Sequence Tag Consensus Map
Genetics,
January 1, 2006;
172(1):
533 - 546.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Wawrzynska, M. Lewandowska, M. J. Hawkesford, and A. Sirko
Using a suppression subtractive library-based approach to identify tobacco genes regulated in response to short-term sulphur deficit
J. Exp. Bot.,
June 1, 2005;
56(416):
1575 - 1590.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. E. Zanetti, I.-F. Chang, F. Gong, D. W. Galbraith, and J. Bailey-Serres
Immunopurification of Polyribosomal Complexes of Arabidopsis for Global Analysis of Gene Expression
Plant Physiology,
June 1, 2005;
138(2):
624 - 635.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. R. Schulze, D. A. R. Sinclair, K. A. Fitzpatrick, and B. M. Honda
A Genetic and Molecular Characterization of Two Proximal Heterochromatic Genes on Chromosome 3 of Drosophila melanogaster
Genetics,
April 1, 2005;
169(4):
2165 - 2177.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
I.-F. Chang, K. Szick-Miranda, S. Pan, and J. Bailey-Serres
Proteomic Characterization of Evolutionarily Conserved and Variable Proteins of Arabidopsis Cytosolic Ribosomes
Plant Physiology,
March 1, 2005;
137(3):
848 - 862.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. F. Pendle, G. P. Clark, R. Boon, D. Lewandowska, Y. W. Lam, J. Andersen, M. Mann, A. I. Lamond, J. W. S. Brown, and P. J. Shaw
Proteomic Analysis of the Arabidopsis Nucleolus Suggests Novel Nucleolar Functions
Mol. Biol. Cell,
January 1, 2005;
16(1):
260 - 269.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Casati and V. Walbot
Crosslinking of Ribosomal Proteins to RNA in Maize Ribosomes by UV-B and Its Effects on Translation
Plant Physiology,
October 1, 2004;
136(2):
3319 - 3332.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
D. L. Remington, T. J. Vision, T. J. Guilfoyle, and J. W. Reed
Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families
Plant Physiology,
July 1, 2004;
135(3):
1738 - 1752.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
V. Leh-Louis, B. Wirth, L. Despons, S. Wain-Hobson, S. Potier, and J. L. Souciet
Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny
Nucleic Acids Res.,
April 15, 2004;
32(7):
2069 - 2078.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Turck, F. Zilbermann, S. C. Kozma, G. Thomas, and F. Nagy
Phytohormones Participate in an S6 Kinase Signal Transduction Pathway in Arabidopsis
Plant Physiology,
April 1, 2004;
134(4):
1527 - 1535.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
R. A. Volkov, I. I. Panchuk, and F. Schoffl
Heat-stress-dependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR
J. Exp. Bot.,
October 1, 2003;
54(391):
2343 - 2349.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
X. Liu and W. V. Baird
The ribosomal small-subunit protein S28 gene from Helianthus annuus (Asteraceae) is down-regulated in response to drought, high salinity, and abscisic acid
Am. J. Botany,
April 1, 2003;
90(4):
526 - 531.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Hoth, M. Morgante, J.-P. Sanchez, M. K. Hanafey, S. V. Tingey, and N.-H. Chua
Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant
J. Cell Sci.,
March 14, 2003;
115(24):
4891 - 4900.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Knappe, U.-I. Flugge, and K. Fischer
Analysis of the Plastidic phosphate translocator Gene Family in Arabidopsis and Identification of New phosphate translocator-Homologous Transporters, Classified by Their Putative Substrate-Binding Site
Plant Physiology,
March 1, 2003;
131(3):
1178 - 1190.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
O. Lecompte, R. Ripp, J.-C. Thierry, D. Moras, and O. Poch
Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale
Nucleic Acids Res.,
December 15, 2002;
30(24):
5382 - 5390.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E.-P. Journet, D. van Tuinen, J. Gouzy, H. Crespeau, V. Carreau, M.-J. Farmer, A. Niebel, T. Schiex, O. Jaillon, O. Chatagnier, et al.
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis
Nucleic Acids Res.,
December 15, 2002;
30(24):
5579 - 5592.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
