Skip to main content
Plant Physiology logoLink to Plant Physiology
. 2001 Oct;127(2):398–415.

The Organization of Cytoplasmic Ribosomal Protein Genes in the Arabidopsis Genome1

Abdelali Barakat 1,2, Kathleen Szick-Miranda 1,2, Ing-Feng Chang 1, Romain Guyot 1, Guillaume Blanc 1, Richard Cooke 1, Michel Delseny 1,3, Julia Bailey-Serres 1,3,*
PMCID: PMC125077  PMID: 11598216

Abstract

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.


The eukaryotic ribosome is a complex structure composed of four rRNAs and about 80 ribosomal proteins (r-proteins). It represents an essential piece of the cell machinery, responsible for protein synthesis, and as such plays a major role in controlling cell growth, division, and development. For example, previous studies have shown that genetic defects in ribosomal components, such as reduction of the levels of individual r-proteins, can cause deleterious effects on the development and physiology of an organism. In Drosophila melanogaster, mutations in r-proteins genes cause the haplo-insufficient Minute phenotype with reduced growth and cell division rates, characterized by a reduced body size and short, thin bristles (Lambertsson, 1998). In contrast, a conditional deletion in the gene encoding r-protein S6 in adult mice (Mus musculus) affects cell cycle progression but not cell growth (Volarevic et al., 2000). In humans, a quantitative reduction in synthesis of the X-linked form of r-protein S4 is observed in individuals with Turner syndrome (monosomic for X) and may contribute to this complex phenotype, which includes short stature and infertility (Zinn and Ross, 1998). In plants, mutations in r-protein genes affect embryo viability or plant development (Van Lijsebettens et al., 1994; Tsugeki et al., 1996; Revenkova et al., 1999; Ito et al., 2000). In addition, a positive correlation was reported between the level of r-protein gene transcript accumulation and cell division in suspension culture cells (Joanin et al., 1993; Garo et al., 1994) or tissues such as auxin-treated hypocotyls, apical meristems, young leaves, and lateral roots (Gantt and Key, 1985; Williams and Sussex, 1995).

Numerous analyses on prokaryotic ribosomes and r-proteins have provided significantly to our knowledge of ribosome structure and composition. Three-dimensional structures of the 30S and 50S ribosomal subunits of thermophilic eubacteria (30S, Thermus thermophilus; 50S, Haloarcula marismortui) have recently been described at 5.5- and 2.5-Å resolution, respectively, from crystallographic data (Ban et al., 1999, 2000; Clemons et al., 1999). In Escherichia coli, 55 r-proteins have been identified and their amino acid sequences determined (Wittmann, 1982; Wittmann-Liebold et al., 1990). The ordered assembly process of eubacterial ribosomes is also reasonably well known (Nomura et al., 1984; Culver et al., 1999). It is generally accepted that ribosomes of an archaebacterial ancestor gave rise to the cytosolic ribosomes of eukaryotes (Matheson et al., 1990; Wittmann-Liebold et al., 1990; Wool et al., 1995). By contrast, the r-proteins of plastids and mitochondria show strong evolutionary similarity to those of eubacteria and include organelle-specific proteins (Graack and Wittmann-Liebold, 1998; Koc et al., 2000; Yamaguchi and Subramanian, 2000; Yamaguchi et al., 2000). In eukaryotes, the protein composition of rat (Rattus norvegicus) ribosomes was determined by direct protein sequencing followed by gene cloning and a presumed complete set of 79 proteins was compiled (Wool et al., 1995). In addition, genes corresponding to 78 Saccharomyces cerevisiae r-proteins were identified through genome sequencing efforts (Goffeau et al., 1996; Planta and Mager, 1998). Eukaryotic r-proteins can be classified based on homology to r-proteins of archae- and eubacteria (Wool et al., 1995). The 80S rat ribosome contains 33 proteins for which orthologues can be found in eubacteria, archaebacteria, and eukaryotes (Group I); 35 proteins with orthologues in archaebacteria and other eukaryotes (Group II); and 21 proteins that appear to be unique to eukaryotes (Group III). The striking evolutionary conservation of r-proteins is not surprising given the constraints of rRNA-protein interactions, coordinated ribosome assembly, and ribosome function. In fact, phylogenetic relationships between animal, fungi, and plant kingdoms have been inferred from comparison of orthologous r-proteins (Veuthey and Bittar, 1998).

The expression and distribution of r-protein genes of both prokaryotes and eukaryotes has also been examined. In eubacteria, most of the r-protein genes are clustered in a few operons, which allows for coordinated regulation (Nomura et al., 1984). Kenmochi et al. (1998b) recently mapped 75 human r-protein genes and showed that they are distributed over all chromosomes, with a bias toward chromosome 19. Synthesis of r-proteins in eukaryotes undoubtedly requires coordination of now unlinked genes. It is striking that the regulation of r-protein gene expression appears to occur at the transcriptional level in yeast (Saccharomyces cerevisiae; Planta and Mager, 1998) and predominantly at the translational level in animals (Meyuhas, 2000; Meyuhas and Hornstein, 2000).

In contrast to the information available on r-proteins and r-protein genes in prokaryotes and a few eukaryotic models (rats and yeast), limited information is available on r-proteins and the number, distribution, and expression of r-protein genes in plants. Gantt and Key (1983) resolved 40 and 51 proteins of the small (40S) and large (60S) subunits of the cytosolic ribosomes of soybean (Glycine max) by two-dimensional gel electrophoresis. In addition, plant genes encoding 77 orthologues to rat cytosolic r-proteins were identified (Bailey-Serres, 1998), including an r-protein (P3) that is apparently limited to plants (Szick et al., 1998). Information describing the genomic distribution of r-protein genes in plants is limited to the mapping of 57 loci for r-protein genes in rice (Oryza sativa; Wu et al., 1995). However, because this study relied on RFLPs, many loci may have been missed due to lack of polymorphism and cross hybridization between members of gene families. Reconstruction of full-length Arabidopsis r-protein cDNAs from redundant overlapping expressed sequence tags (ESTs) demonstrated that the occurrence of small gene families with several transcribed genes seems to be the rule rather than an exception (Cooke et al., 1997).

Several studies on plant r-protein genes have revealed the presence of multigene families in which members show both overlapping and differential patterns of mRNA accumulation (Larkin et al., 1989; Van Lijsebettens et al., 1994; Williams and Sussex, 1995; Dresselhaus et al., 1999; Revenkova et al., 1999). Evidence that r-protein gene expression may be controlled at a posttranscriptional level was observed for L13 in rapeseed (Brassica napus) and Arabidopsis (Saez-Vasquez et al., 2000), P2 in anoxic roots of maize (Zea mays) seedlings (Fennoy and Bailey-Serres, 1998), as well as S4, S6, L3, and L16 following imbibition in embryos of maize (Beltran-Pena et al., 1995). From these analyses, it appears that r-protein expression in plants may be regulated at the transcriptional and posttranscriptional levels.

The international Arabidopsis Genome Initiative (AGI; Bevan et al., 1997; Lin et al., 1999; Mayer et al., 1999; AGI, 2000) has led to the to the accumulation of an enormous quantity of genomic sequence data, in addition to more than 112,500 ESTs (Höfte et al., 1993; Newman et al., 1994; Cooke et al., 1996; Asamizu et al., 2000). The essentially complete genome sequence is publicly accessible through The Arabidopsis Information Resource (TAIR) database (http://www.Arabidopsis.org/). This situation provided a unique opportunity for analyzing r-protein gene number, chromosomal location, and expression. Here, we report the identification and map positions of 249 r-protein genes of Arabidopsis. Location of the genes was initially determined by physical mapping using ESTs and subsequently confirmed from the genomic sequence data, in some cases of genomic regions that were not completely annotated. Analysis of r-protein gene distribution initially allowed us to discover duplications of several very large DNA sequences, which shed light on Arabidopsis genome evolution (Blanc et al., 2000). Comparison of the distribution of these gene families in the Arabidopsis genome and in other organisms and its implications on the understanding of multigene family organization and genome evolution are discussed. The systematic identification of ESTs representing different gene family members as well as reverse transcriptase (RT)-PCR on RNA obtained from different tissues and PCR on a cDNA library (Newman et al., 1994) revealed that levels of r-protein pseudogenes are very low and indicated that many of genes family members are differentially expressed. Variation in r-protein gene family member sequences and expression patterns raises the possibility of ribosome heterogeneity at subcellular and intracellular levels.

RESULTS

Identification of 249 Cytoplasmic r-Protein Genes in Arabidopsis

To identify r-protein genes in the Arabidopsis genome, we chose rat as the eukaryotic model because its r-protein genes have been extensively studied and corresponding genes in plants had been identified (Bailey-Serres, 1998). We collected all 79 rat r-protein sequences from the Swiss-PROT library (Bairoch and Apweiler, 2000) and carried out TBLASTN (Altschul et al., 1997) searches on Arabidopsis EST and cDNA sequences in GenBank (Release 65.0, November 2000). Most of the 79 rat protein genes had several orthologues in Arabidopsis based on high probability BLAST scores (data not shown). An estimate of the number of expressed genes in each family was determined by constructing contigs from ESTs. The accuracy of EST contig construction was tested as described by Cooke et al. (1997) and redundancy within families was eliminated by careful comparison of the contigs to one another and to genomic sequences. In this manner, we identified 200 r-protein genes. In addition, TBLASTN alignment against Arabidopsis genomic sequence data released through the AGI allowed us to identify a total of 249 r-protein genes, including 101 encoding 32 putative small-subunit proteins and 148 encoding 48 putative large-subunit proteins (Table I). Genes identified from ESTs and genomic sequences were compared and a nonredundant set of r-proteins was collated. A perfect match to a genomic sequence was found for all 200 EST contigs. Therefore, this approach revealed an additional 49 genomic sequences that were not identified by EST contigs, including those that appear to contain an incomplete ORF. This analysis also resulted in discovery of 36 r-protein genes that were not detected by automated annotation or in which the annotation was incorrect (Table I, indicated with an asterisk after the gene name). Because no orphaned EST contigs were identified, it seems unlikely that additional r-protein genes will be identified in the centromeric regions that have not been fully sequenced.

Table I.

Identification of Arabidopsis orthologues of rat small (40S) and large (60S) ribosomal subunit proteins

r-Protein
Evolutionary Group Genomic
MATDB AGI Gene Name EST
Chromosome No. Mbp Nearest Marker
Deduced Polypeptide
Protein name Gene name GenBank accession no. Clone position GenBank accession no. Frequency Marker name Map position % ID rat kD Amino acids pI
Sa RPSaA I AC016529 T10D10.16 At1g72370 T14000 22 1 27.0 nga111 115.5 54.1 32.3 298 4.9
RPSaB AC011437 F7O18.26 At3g04770 U66223 1 3 1.25 GAPC 8.4 56.9 30.7 280 4.9
S2 RPS2A I AC082643 F9K23.9 At1g58380 AV550768 3 1 21.3 SGCSNP301 85.9 75.3 30.7 284 11.0
RPS2B AC027036 T4M14.3 N.A. N.F. 0 1 21.4 ARR3 87 76.3 30.8 284 11.0
RPS2C AC002339 T11A7.6 At2g41840 B10274 5 2 17.7 COR15 76.8 74.5 30.9 285 11.1
RPS2D AL133248 T8H10.90 At3g57490 F14347 2 3 21.8 SNP7 77 74.9 30.1 276 11.0
S3 RPS3A I AC007071 T9H9.13 At2g31610 AV553035 7 2 13.7 nga361 63 81.5 27.5 250 10.4
RPS3B AL132960 F5K20.170 At3g53870 T04067 17 3 20.4 AFC1 73.9 81.9 27.3 249 10.4
RPS3C AB015477 MOK9.14 At5g35530 AV550513 8 5 13.8 PHYC 71.1 76.3 27.5 248 10.4
S3a RPS3aA II AC009465 T9J14.21 At3g04840 AV545036 13 3 1.4 GAPC 8.4 67.6 29.9 262 10.6
RPS3aB AL023094 T4L20.250 At4g34670 AJ001342 2 4 15.8 g3088 83.3 69.6 29.8 262 10.5
S4 RPS4A* II AC002329 F5J6.12 At2g17360 F20029 7 2 7.8 m216 33.1 69.7 30.1 263 11.0
RPS4B AL163652 T28J14.30 At5g07090 AV554668 16 5 2.2 SGCSNP21 18 69.8 29.9 262 10.9
RPS4C* AB017068 MJG14.8 N.A. N.F. 0 5 14.8 gln1-1 77.3 iORF
RPS4D* AB025632 MQJ2.2 At5g58420 AV551244 14 5 23.7 mi184 113.7 69.8 29.8 262 11.0
S5 RPS5A I AC005896 F3G5.6 At2g37270 AI099638 8 2 15.9 Ve018 69.7 78.0 23.0 207 10.5
RPS5B AC016795 F26K24.23 At3g11940 BE038477 20 3 3.7 SGCSNP245 14.8 76.7 22.9 207 10.4
S6 RPS6A II AL031004 F28M20.110 At4g31700 AV550020 6 4 14.5 g8300 81.2 67.6 28.4 250 11.4
RPS6B AL353995 F12B17.290 At5g10360 AV37347 18 5 3.4 ve033 25.42 67.6 28.1 249 11.5
S7 RPS7A III AC073555 F11I4.1 N.A. AV549012 4 1 17.6 mi441 72.9 55.4 21.9 191 10.6
RPS7B AC021640 F16B3.19 At3g02560 Z47625 2 3 0.5 MI74B 5.8 53.8 22.2 191 10.6
RPS7C AL391148 T21H19.50 At5g16130 AV544115 5 5 5.3 nga106 33.3 54.3 22.1 190 10.6
S8 RPS8A* II AF296825 F5O24 At5g20290 BE037738 10 5 6.9 mi433 42.2 62.4 24.1 213 11.2
RPS8B AB016890 MNC17.15 At5g59240 AI999676 E 5 24.0 mi184 113.7 64.5 23.8 210 11.3
S9 RPS9A I AL161533 F16J13.230 At4g12160 N.F. 0 4 6.4 g4108 43.5 iORF
RPS9B AL353993 F8M21.90 At5g15200 AV54959 30 5 5.0 SNP13 30.3 74.7 23.0 198 10.9
RPS9C AB010077 MYH19.1 At5g39850 AV010077 1 5 16.1 SNP150 83.2 74.2 23.2 197 11.1
S10 RPS10A III AL049480 F14M19.20 At4g25740 AI997138 6 4 12.4 RPS2 75.6 58.9 19.4 177 10.5
RPS10B AB005233 MBK23.4 At5g41520 AV536209 11 5 16.7 g4028 86.2 52.9 19.7 180 10.6
RPS10C AB025606 F6N7.14 At5g52650 AI999527 4 5 21.4 SGCSNP242 107.1 53.5 19.8 181 10.4
S11 RPS11A I AL132967 T2J13.230 At3g48930 Z26185 5 3 18.6 SGCSNP352 68.3 61.0 18.0 160 11.3
RPS11B AL022198 F6I18.290 At4g30800 N.F. E 4 14.3 PRHA 78.9 64.7 17.9 159 11.5
RPS11C AB005244 MRO11.22 At5g23740 AV561164 2 5 8.2 CDPK9 44.5 61.4 17.7 159 11.4
S12 RPS12A III AC010924 T24D18.3 At1g15930 T14030 9 1 5.5 srp54a 18.9 52.6 15.4 144 5.3
RPS12B AC011713 F23A5.10 At1g80750 N.F. 0 1 30.1 mi157 124.3 iORF
RPS12C AC006223 F22D22.19 At2g32060 AI999579 6 2 13.9 ASP1 62.7 52.6 15.3 144 5.8
S13 RPS13A I AL162295 T4C21.180 At3g60770 Z17784 10 3 22.9 snp74 84.6 77.3 17.0 150 11.2
RPS13B(A) AF069299 F6N15.7 At4g00100 Z29915 6 4 0.5 NOR4 0.0 78.0 16.9 150 11.2
S14 RPS14A I AC007135 F9C22.9 At2g36160 AV552523 1 2 5.5 ve016 67.6 85.3 16.3 150 11.3
RPS14B AC008153 F24K9.19 At3g11510 R89968 3 3 3.6 SNP245 14.7 85.3 16.3 150 11.3
RPS14C AL050300 F2206.40 At3g52580 AV55346 3 3 19.9 mi456 72.7 85.3 16.2 150 11.3
S15 RPS15A I AC000104 F19P19.29 At1g04270 AV544758 17 1 1.1 SGCSNP151 3.3 75.4 17.1 152 11.1
RPS15B AL391712 T5E8.290 At5g09490 N.F. 0 5 2.9 ve033 25.4 71.7 17.1 152 10.9
RPS15C AL391712 T5E8.300 At5g09500 N.F. 0 5 2.9 ve033 25.4 73.9 16.7 150 11.3
RPS15D AL391712 T5E8.310 At5g09510 AV549585 6 5 2.9 ve033 25.4 75.4 17.1 152 11.1
RPS15E AB016875 K9D7.14 At5g43640 N.F. 0 5 17.6 mi194 90.5 74.7 16.8 149 11.3
RPS15F AB008265 MCD12.3 At5g63070 N.F. 0 5 25.3 mi211A 119 iORF
S15a RPS15aA I AC007583 F24B9.12 At1g07770 AV538172 9 1 2.5 ve004 7.76 77.7 14.8 130 10.7
RPS15aB AC005169 F6F22.25 At2g19720 Z26126 1 2 8.9 MI148 36.1 47.6 14.7 129 10.6
RPS15aC AC004218 F12L6.25 At2g39590 N.F. NE 2 16.8 M429 73.1 73.1 15.3 130 10.0
RPS15aD AL355775 F12M12.10 At3g46040 AW004284 3 3 17.5 M249 61.3 77.7 14.8 130 10.8
RPS15aE AL161575 F27B13 At4g29430 N.F. 0 4 13.8 prha 78.9 48.0 14.9 129 10.7
RPS15aF AB015475 MMN10.8 At5g59850 AV554198 7 5 24.2 SNP2 115.9 77.7 14.8 130 10.7
S16 RPS16A I AC006586 F7B19.13 At2g09990 AV536848 2 2 4.1 mi421 19.1 73.3 16.6 146 11.0
RPS16B AC016829 T6K12.15 At3g04230 Z17479 2 3 1.1 GAPC 8.4 73.3 16.6 146 11.0
RPS16C* AC051626 F20L16 At5g18380 AV534112 1 5 6.1 GDH1 33.29 74.0 16.6 146 11.0
S17 RPS17A II AC006951 T1O3.20 At2g04390 AV550538 3 2 1.6 Igs1 13.2 61.1 16.0 141 10.8
RPS17B* AC007018 F5G3.12 At2g05220 AV534112 7 2 1.9 m497A 13.3 61.9 16.0 140 10.8
RPS17C AC011560 F13M14.10 At3g10610 AV534760 4 3 3.3 SNP11 14.7 60.2 16.0 140 10.8
RPS17D AB008271 MUK11.12 At5g04800 AV553023 8 5 1.4 nga225 14.3 61.1 16.0 141 10.8
S18 RPS18A (A) I AC003979 T22J18.5 At1g22780 AV552655 12 1 8.1 m235 34.0 74.3 17.5 152 11.3
RPS18B (B) AC015446 F12G12.15 At1g34030 BE037678 10 1 12.5 AIG1 55.62 74.3 17.5 152 11.3
RPS18C (C) AL049482 F17A8.150 At4g09800 AV530846 4 4 5.4 DET1 31.4 74.3 17.5 152 11.3
S19 RPS19A II AC011664 F1C9.13 At3g02080 AV536148 7 3 0.3 mi74b 5.8 56.9 15.8 143 10.9
RPS19B AL391143 T20K14.130 At5g15520 AV559770 1 5 5.1 nga106 33.2 56.5 15.8 143 11.0
RPS19C AB006696 MAF19.17 At5g61170 AI996699 1 5 24.7 LFY3 116.8 59.0 15.7 143 11.0
S20 RPS20A I AL353992 F14D17.100 At3g45030 AV353992 3 3 16.9 TOPP5 59.2 74.1 13.1 117 10.5
RPS20B* AL096860 T21L8.120 At3g47370 AV532791 3 3 17.9 ASN1 61.4 74.1 13.7 117 10.5
RPS20C AB019235 MMI9.13 At5g62300 AV533085 3 5 25.1 LFY3 116.8 74.1 13.1 117 10.5
S21 RPS21A* III AB024028 K1G2 At3g27450 N.F. 0 3 10.1 mi287 43.6 iORF
RPS21B AL132960 F5K20.190 At3g53890 AI997498 2 3 20.4 Ve042 76.2 46.3 9.1 82 8.1
RPS21C* AC069556 T1G16 At5g27700 AV536952 6 5 9.9 SO262 65.2 43.8 9.0 81 8.4
S23 RPS23A* I AC016661 F11F8.27 At3g09680 N.F. 0 1 2.9 mi357 16.2 76.1 15.8 142 11.1
RPS23B AL162973 F9G14.270 At5g02960 AV553972 19 5 0.6 SNP241 3.7 78.9 16.2 146 11.1
S24 RPS24A II AC009465 T9J14.13 At3g04920 BE038406 4 3 1.4 GAPC 8.4 67.5 15.4 133 11.0
RPS24B* AC007627 F15F15 At5g28060 BE037704 4 5 10.1 SO262 65.2 65.1 15.4 133 11.3
S25 RPS25A III AC007047 F16F14.14 At2g16360 N.F. NE 2 7.4 mi398 29.2 iORF
RPS25B AC007119 F2G1.15 At2g21580 BE038441 19 2 9.5 mi238 39.9 59.4 12.1 108 11.5
RPS25C AP002066 T4A2.5 At3g30740 N.F. 0 3 12.4 atpox 52.4 iORF
RPS25D AL023094 T4L20.250 At4g34670 N.F. 0 4 15.7 SNP232 83.4 iORF
RPS25E AL050351 T22F8.100 At4g39200 AV533470 29 4 17.5 AP2 95.9 58.5 12.1 108 11.5
S26 RPS26B III AC002336 T2P4.14 At2g40510 BE038315 11 2 17.2 g4514 73.7 67.3 14.8 133 11.7
RPS26A AC002336 T2P4.6 At2g40590 Z26184 1 2 17.2 g4514 73.7 67.3 14.8 133 11.7
RPS26C AL163763 F18O21.300 At3g56340 AI998355 11 3 21.3 SNP189 77.2 70.9 14.6 130 11.7
S27 RPS27A (C) II AC004665 F4I18.31 At2g45710 AA712867 4 2 19.1 ve019 82.1 75.3 9.5 84 9.1
RPS27B (A) AL137898 T20K12.10 At3g61110 AL137898 6 3 23.2 SNP221 85.8 77.9 9.5 85 8.7
RPS27C (ϕ)* AL137898 T20K12 N.A. N.F. 0 3 23.2 SNP221 85.8 iORF
RPS27D (B) AB024025 K16F13.1 At5g47930 AV531451 12 5 19.5 SGCSNP147 99.5 79.2 9.5 84 9.1
S27a RPS27aA II AC007945 F28C11.5 At1g23410 Z25557 2 1 8.4 m235 34 81.4 17.7 156 10.6
RPS27aB AC004411 F14M4.6 At2g47100 AV548497 3 2 19.6 Athb7 84.5 84.9 17.8 157 10.6
RPS27aC AL138651 T17J13.210 At3g62250 AA728493 6 3 23.5 mi424 82.8 84.2 17.8 157 10.6
S28 RPS28A II AC010927 T22K18.8 At3g10090 N.F. NE 3 3.1 mi357 16.2 78.3 7.4 64 11.5
RPS28B AB005235 MED24.15 At5g03850 AV530936 2 5 1.9 SGCSNP396 9.28 78.3 7.4 64 11.5
RPS28C AB008266 MHJ24.12 At5g64140 Z17569 2 5 25.7 ve032 123.3 80.0 7.3 64 11.7
S29 RPS29A I AL163975 T15B3.120 At3g43980 T22180 3 3 16.2 TOPP5 59.2 72.2 6.4 56 10.8
RPS29B AL163975 T15B3.150 At3g44010 Z47604 3 3 16.2 TOPP5 59.2 72.2 6.4 56 10.8
RPS29C* AL161584 F17I5 N.A. AI996253 5 4 15.5 pCITd104 83.3 70.4 6.1 54 10.9
RPS29D* AL161584 F17I5 N.A. N.F. 0 4 15.5 pCITd104 83.3 iORF
S30 RPS30A* II AC005169 F6F22.22 At2g19750 AV532814 4 2 8.9 mi148 36.1 75.9 6.9 62 12.8
RPS30B AL161575 F19B15 At4g29390 N.F. 0 4 13.5 mi232 76.7 76.3 6.9 62 12.8
RPS30C AB013392 M1K19.12 At5g56670 AI100293 2 5 23.0 mi69 114.3 75.9 6.9 62 12.8
P0 RPP0A I AF002109 T28M21.17 At2g40010 N.F. 0 2 16.9 SGCSNP214 74.7 51.6 33.7 317 5.0
RPP0B AC011436 F3L24.7 At3g09200 T21000 40 3 2.8 mi467 15.6 53.8 34.1 320 4.8
RPP0C AC073395 F11B9.17 At3g11250 AV561267 6 3 3.5 SGCSNP11 14.7 55.7 34.4 323 4.9
P1 RPP1A I AC007323 T25K16.9 At1g01100 AV536016 4 1 12.1 Ve001 2.9 58.2 11.2 112 4.1
RPP1B AL161472 T18A10.9 At4g00810 AV522332 3 4 0.3 mi122 5 56.1 11.0 110 4.0
RPP1C AB016886 MCA23.2 At5g47700 AV530633 3 5 19.4 SGCSNP147 99.4 57.7 11.2 113 4.1
P2 RPP2A I AC005824 F15K20.18 At2g27720 AV532448 17 2 12.0 nga1126 50.6 50.4 11.4 115 4.4
RPP2B AC005824 F15K20.19 At2g27710 AV535852 13 2 12.0 nga1126 50.6 50.4 11.4 115 4.4
RPP2C AP002059 T20D4.1 At3g28500 F19923 2 3 10.7 AIG2 50.59 39.1 11.7 115 4.4
RPP2D AL353818 F14L2.140 At3g44590 AV534715 2 3 16.6 m249 61.3 57.7 11.0 111 4.2
RPP2E AB022222 MUD12.2 At5g40040 Z17443 2 5 16.1 SGCSNP150 83.2 53.2 11.8 114 4.3
P3 RPP3A I AL049480 F14M19 At4g25890 AV556500 1 4 12.3 RSP2 75.6 Planta 11.8 119 4.2
RPP3B AB019233 MJB24.10 At5g57290 AV535058 7 5 23.3 m558a 113.8 Planta 11.9 120 4.3
L3 RPL3A (1) I AC005687 F1I21.L3 At1g43170 AV562764 21 1 15.8 SGCSNP163 63 66.2 44.6 389 11.0
RPL3B(2) AC005850 T25B24.7 At1g61580 AV557676 1 1 22.3 mi230 86.5 67.4 44.5 390 11.1
RPL3C AB016888 MDH9.14 N.A. N.F. E 5 17.0 DFR 89.5 iORF
L4 RPL4A II AC016661 F11F8.22 At3g09630 AV551524 8 1 2.9 APX1B 16.2 58.1 44.7 406 11.1
RPL4B AC079605 T32G9.26 At1g35200 N.F. 0 1 12.9 mi342 58.7 iORF
RPL4C AC007266 F27A10.4 N.A. N.F. 0 2 10.7 SNP203 44.4 iORF
RPL4D AL162973 F9G14.180 At5g02870 AV541474 6 5 0.6 SNP241 3.7 56.7 44.7 407 11.1
L5 RPL5A I AB025639 MWL2.17 At3g25520 AV5645486 5 3 9.2 m433 38 57.0 34.2 300 10.1
RPL5B AB016876 MKM21.5 At5g39740 AV525399 9 5 16.0 SGCSNP150 83.2 57.3 34.4 301 10.0
RPL5C AB010699 MSN9.3 At5g40130 N.F. 0 5 16.1 SGCSNP164 83.7 iORF
L6 RPL6A III AC026238 F25I16.12 At1g18540 AV566810 22 1 6.4 mi348 23.6 52.6 26.2 233 10.9
RPL6B AC016662 F2P9.7 At1g74060 H36726 6 1 27.5 bw54 116 54.4 26.0 233 11.2
RPL6C AC016662 F2P9.8 At1g74050 AV442576 11 1 27.5 bw54 116 54.8 26.1 233 11.2
L7 RPL7A I AC011713 F23A5.10 At1g80750 AV561722 1 1 30.1 SGCSNP355 131.1 37.7 28.3 247 10.5
RPL7B AC006200 F10A8.13 At2g01250 AV550374 6 2 0.2 rga 1.7 60.8 28.1 242 10.7
RPL7C AC004005 F6E13.25 At2g44120 AI100283 3 2 18.4 m336 79 60.3 28.5 242 10.7
RPL7D AP002038 K20M4.2 At3g13580 N.F. 0 3 4.4 nga162 20.5 61.7 28.4 240 10.8
L7a RPL7aA II AC002535 T30B22.8 At2g47610 T76559 7 2 19.7 mi79a 87.5 57.9 29.1 257 10.9
RPL7aB AL162651 F26K9.300 At3g62870 AV536728 16 3 23.7 SNP264 89.3 57.1 29.0 256 11.0
L8 RPL8A I AC006201 T27K22.11 At2g18020 T44362 8 2 8.1 m216 33.1 71.4 27.9 258 11.6
RPL8B AL132980 F24M12.230 At3g51190 N.F. 0 3 19.5 MUR 1 72.7 71.0 28.0 260 11.3
RPL8C AL022141 F23E13.20 At4g36130 H37035 8 4 16.3 fah1 86.3 70.6 27.9 258 11.5
L9 RPL9A I AC027035 T16O9.23 N.A. AV533409 19 1 12.1 mi2532 51.8 57.1 22.0 194 10.2
RPL9B AC021045 T9L6.2 At1g33120 AV549042 15 1 12.0 mi2532 51.8 57.1 22.0 194 10.2
RPL9C AC021045 T9L6.5 At1g33140 AV549555 28 1 12.0 mi2532 51.8 57.1 22.0 194 10.2
RPL9D AL049524 F7L13.30 At4g10450 AV541541 6 4 5.6 SGCSNP24 30.88 58.3 22.0 194 10.3
L10 RPL10A II AC012188 F14L17.9 At1g14320 AV553316 25 1 4.9 SGCSNP303 14.6 69.9 24.9 220 11.3
RPL10B AC005508 T2P11.10 At1g26910 N.F. E 1 9.4 mi192 41.1 69.4 24.9 221 11.2
RPL10C* AC079285 T12I7.3 At1g66580 AI998557 3 1 24.4 mi185 102.1 69.8 24.1 214 11.3
L10a RPL10aA* I AC006932 T27G7.6 At1g08360 AV554254 14 1 2.6 SGCSNP308 0.89 63.0 24.3 215 10.7
RPL10aB* AC005824 F15K20.37 At2g27530 AV551399 11 2 12.1 ngal126 50.65 64.2 24.3 215 10.7
RPL10aC AB007651 MWD9.24 At5g22440 AV553355 16 5 7.5 mi433 42 62.8 24.5 217 10.6
L11 RPL11A(A) I AC006931 F7D19.26 At2g42740 N.F. 0 2 18.0 COR15 76.8 72.0 20.9 182 10.7
RPL11B AL353032 T20N10.50 At3g58700 Z29916 3 3 22.2 SNP7 77.1 70.1 20.9 182 10.8
RPL11C(B) AL035526 F28A21.140 At4g18730 AA712813 18 4 9.4 AG 63 70.3 21.1 184 10.8
RPL11D AB012245 MRA19.21 At5g45775 AV532938 6 5 18.5 mi61 98.1 70.1 20.9 182 10.8
L12 RPL12A I AC006260 T2N18.5 At2g37190 AV540047 5 2 15.8 ve018 69 70.6 18.0 166 9.6
RPL12B AL132966 F4P12.130 At3g53430 BE038784 8 3 20.2 AFC1 73.9 69.3 18.0 166 9.6
RPL12C AB005246 MUP24.9 At5g60670 AV530701 7 5 24.4 SGCSNP2 115.9 69.9 17.8 166 9.6
L13 RPL13A III AL096856 T24C20.10 At3g48130 N.F. 0 3 18.3 m409 64 iORF
RPL13B AL132967 T2J13.150 At3g49010 AV553216 10 3 18.6 SGCSNP291 68.2 55.2 23.8 206 11.7
RPL13C AL132967 T2J13.200 At3g48960 Z34694 18 3 18.6 SGCSNP291 68.2 51.2 23.5 206 11.3
RPL13D AB005244 MRO11.6 At5g23900 AI100098 11 5 8.1 CDKP9 44.5 57.1 23.5 206 11.7
L13a RPL13aA I AC012395 T1B9.24 At3g07110 AV541696 14 3 2.3 SGCSNP115 3.32 60.5 23.5 206 11.2
RPL13aB AB028609 K7P8.12 At3g24830 AA042521 4 3 9.1 g4711 38 60.5 23.5 206 11.1
RPL13aC AL049751 F17N18.60 At4g13170 AI999348 1 4 6.8 mi465 45 61.1 23.6 206 11.2
RPL13aD AB012242 K24G6.9 At5g48760 AV542288 6 5 19.9 M331 102.6 60.5 23.6 206 11.2
L14 RPL14A III AC007109 T13C7.4 At2g20450 N.F. 0 2 9.1 SNP71 35.8 46.9 15.5 134 10.9
RPL14B AL161566 T24A18.40 At4g27090 BE038422 8 4 12.8 mi123 75.6 44.6 15.5 134 10.8
L15 RPL15A III Z97341 FCA6 At4g16720 BE039553 6 4 ∼8.0 SGCSNP272 56 70.4 24.2 204 12.0
RPL15B* Z97343 FCA8 At4g17390 AV549804 7 4 ∼8.0 mi112 58.1 70.0 24.2 204 12.0
L17 RPL17A I AC004557 F17L21.19 At1g27400 AI996162 8 1 9.6 ve008 47.7 66.7 19.3 172 11.0
RPL17B AC004393 T1F15.11 At1g67430 BE03992 12 1 25.0 mi185 102.2 67.3 19.9 175 10.9
L18 RPL18A II AC002535 T30B22.13 At2g47570 N.F. E 2 19.7 mi79a 87 62.5 20.8 187 11.3
RPL18B AC011620 F18C1.14 At3g05590 AV550190 6 3 1.7 mi355 13.9 64.9 20.9 187 11.7
RPL18C* AC007399 F14I23 At5827850 AV552450 8 5 10.0 SO262 65.2 63.8 20.9 187 11.7
L18a RPL18aA* II AC022455 T1P2.8 At1g29970 N.F. 0 1 10.5 m215 41.6 53.3 21.4 178 11.2
RPL18aB AC004077 T31E10.18 At2g34480 AV549659 12 2 14.8 ve016 67.6 53.3 21.3 178 11.3
RPL18aC AB023038 MIE1.10 At3g14600 AV542705 3 3 4.8 SNP20 20 51.5 21.3 178 11.1
L19 RPL19A II AC009525 F22D16.23 N.A. AV536229 25 1 0.7 GST1 3.9 68.9 24.6 214 12.0
RPL19B AB022217 MGL6.25 At3g16780 AV549838 3 3 5.7 m228 23 69.5 24.3 209 11.9
RPL19C AF075597 T2H3.3 At4g02230 T04719 5 4 1.0 ve023 11.9 71.2 23.3 200 12.0
L21 RPL21A II AC003970 F14J9.25 At1g09590 AV552764 5 1 3.0 phyA 11.3 48.7 18.7 164 11.3
RPL21B* AC003970 F14J9 N.A. N.F. 0 1 3.0 phyA 11.3 iORF
RPL21C AC000132 F21M12.8 At1g09690 AV537606 7 1 3.1 ve005 11.4 48.7 18.7 164 11.3
RPL21D AC007654 T19E23.15 N.A. BE527706 2 1 11.2 UFO 47 iORF
RPL21E AC079733 T8L23.13 At1g57660 R65045 7 1 20.9 nga280 83.8 48.7 18.7 164 11.3
RPL21F AL132977 T10K17.30 At3g57820 AA585876 1 3 21.9 SNP7 77.1 iORF
L22 RPL22A III AC009525 F22D16.17 At1g02830 N.F. NE 1 0.6 GST1 3.9 58.4 14.5 127 10.6
RPL22B AC011620 F18C1.17 At3g05560 T88520 1 3 1.7 mi355 13.9 68.7 14.0 124 10.4
RPL22C* AC069556 T1G16 At5g27770 Z33746 1 5 9.8 SO262 65.2 64.1 14.0 124 10.1
L23 RPL23A* I AC000104 F19P19.5 At1g04480 AV557949 9 1 1.1 SGCSNP151 3.3 84.4 14.5 136 11.1
RPL23B AC002332 F4P9.14 At2g33370 Z33670 10 2 14.4 ve015 63.9 84.9 15.0 140 11.2
RPL23C AC022287 T27C4.4 At3g04400 BE037765 4 3 1.1 GAPC 8.4 84.9 15.0 140 11.2
L23a RPL23aA(2) I AC004218 F12L6.12 At2g39460 BE039409 5 2 16.7 SGCSNP37 72.4 74.8 17.4 154 11.0
RPL23aB(3) AL132954 T26I12.160 At3g55280 AV544539 7 3 20.9 ve022 76.8 74.1 17.9 158 11.0
L24 RPL24A* II AC006282 F13K3.2 At2g36620 AV551827 4 2 15.6 ve017 64.1 47.0 18.4 160 11.5
RPL24B AL132969 F8J2.190 At3g53020 Z26463 4 3 20.1 SGCSNP188 74.4 48.0 18.6 163 11.5
L26 RPL26A I AL132965 T16K5.260 At3g49910 AW004134 6 3 18.9 SGCSNP398 72.2 73.4 16.9 146 11.5
RPL26B AB013390 K9I9.7 At5g67510 Z26419 1 5 27.0 m555 132.6 76.7 16.8 146 11.8
L27 RPL27A III AC006223 F22D22.3 At2g32220 AI995587 2 2 13.8 SGCSNP26 63.27 57.8 15.5 135 11.0
RPL27B AP001306 MKA23.13 At3g22230 AV550432 7 3 7.8 PAP606 30 56.3 15.6 135 11.1
RPL27C AL161540 FCA2 At4g15000 T76226 5 4 ∼7.5 mi198 49.6 55.6 15.6 135 11.1
L27a RPL27aA I AC012187 F13K23.22 At1g12960 N.F. 0 1 4.3 ve006 16.1 61.5 16.5 144 11.0
RPL27aB AC005292 F26F24.13 At1g23290 Z26208 8 1 8.3 m235 34 67.6 16.3 146 11.3
RPL27aC AC010796 F24J13.17 N.A. AV537006 6 1 26.3 mi462 110.7 67.6 16.5 146 11.4
L28 RPL28A III AC005169 F6F22.24 At2g19730 BE038429 4 2 8.8 mi148 36.1 34.9 15.9 143 11.4
RPL28B* AP000600 MAG2 N.A. N.F. 0 3 4.7 nga162 20.5 iORF
RPL28C AL161574 F19B15 At4g29410 AV545939 8 4 13.5 mi232 76.7 35.7 15.9 143 11.6
L29 RPL29A III AC023912 F3E22.16 At3g06700 T46465 3 3 2.1 SGCSNP115 3.32 69.2 7.0 61 12.0
RPL29B AC023912 F3E22.18 At3g06680 N.F. 0 3 2.1 SGCSNP115 3.32 69.2 7.0 61 12.0
L30 RPL30A II AC025781 F15C21.6 At1g36240 N.F. 0 1 13.7 SGCSNP279 61.13 72.5 12.3 112 10.6
RPL30B* AC009243 F28K19.15 At1g77940 AV532452 13 1 29.0 ve011 119.4 69.7 12.4 112 10.1
RPL30C AB026654 MVE11.10 At3g18740 N.F. 0 3 6.4 ve039 24.6 69.7 12.3 112 10.5
L31 RPL31A II AC005169 F6F22.23 At2g19740 AA712836 4 2 8.8 mi148 36.1 58.8 13.7 119 10.7
RPL31B AL049171 T25K17.40 At4g26230 BE526625 2 4 12.4 RPS2 75.6 59.3 13.8 119 10.6
RPL31C AB013392 MIK19.16 At5g56710 AF162852 4 5 23.0 mi69 114.2 57.5 13.8 119 10.7
L32 RPL32A II AL110123 F15J5.70 At4g18100 Z17739 3 4 9.2 mi32 60.9 66.9 15.5 133 11.6
RPL32B AB019223 K11I1.2 At5g46430 AA042212 3 5 18.9 SGCSNP219 96.8 64.6 14.5 133 11.5
L34 RPL34A III AC005508 T2P11.7 At1g26880 F20073 3 1 9.3 mi92 41.1 52.2 13.7 120 12.2
RPL34B AC013289 T6C23.18 At1g69620 AI013289 9 1 26.0 mi462 110.7 51.3 13.7 119 12.2
RPL34C AP000386 MLD15.7 At43g28900 N.F. 0 3 10.9 AIG2 50.5 49.6 13.6 120 12.0
L35 RPL35A I AC016661 F11F8.7 At3g09500 N.F. 0 1 2.9 APX1B 16.2 64.8 14.3 123 11.6
RPL35B AC004218 F12L6.5 At2g39390 BE038438 6 2 16.7 SGCSNP37 72.4 64.8 14.3 123 11.6
RPL35C AL132954 T26I12.50 At3g55170 BE038964 2 3 20.9 SGCSNP134 75.75 63.9 14.2 123 11.6
RPL35D AL162971 T22P11.200 At5g02610 AV549599 6 5 0.5 SNP241 3.7 64.8 14.3 123 11.6
L35a RPL35aA II AC067971 F10K1.22 At1g06980 N.F. 0 1 2.1 GT45 1 8.52 55.9 12.9 112 11.5
RPL35aB AC008046 F5A13.4 At1g41880 AV535617 6 1 15.2 mi133 61 55.9 12.8 111 11.5
RPL35aC AC020579 F1O17.6 At1g74270 N.F. 0 1 27.6 SGCSNP380 117.2 56.9 12.9 112 11.5
RPL35aD AL161667 F1I16.160 At3g55750 AI994336 6 3 21.1 SGCSNP189 77.2 55.9 12.8 111 11.5
L36 RPL36A III AC004684 F13M22.10 At2g37600 AI999791 1 2 16.0 ve018 69.7 58.3 12.7 113 12.3
RPL36B AL132960 F5K20.40 At3g53740 AV533586 14 3 20.3 ve042 76.29 60.0 12.7 112 12.3
RPL36C AL162971 T22P11.40 At5g02450 T04630 2 5 0.5 SGCSNP241 3.7 59.6 12.2 108 12.1
L36a colRPL36aA II AB015474 MLM24.12 At3g23390 AV541635 10 3 8.3 mi386 36.3 76.8 12.1 105 11.1
RPL36aB Z97336 FCA1 At4g14320 BE528949 6 4 7.2 ve024 51.9 76.8 12.1 105 11.1
L37 RPL37A* II AC007591 F9L1 At1g15250 F20017 3 1 5.2 SRP54A 18.9 66.7 10.6 93 12.4
RPL37B AC037424 F19K6.12 At1g52300 AV524548 17 1 19.1 PAP240 81.1 67.4 10.8 95 12.4
RPL37C* AB012247 MSL1 At3g16080 AI998492 5 3 5.4 m228 23.4 63.8 10.7 95 12.4
L37a RPL37aA III AC004667 T4C20.10 N.A. N.F. E 2 15.1 m323 67.9 iORF
RPL37aB AC009991 F9F8.23 At3g10950 N.F. 0 3 3.5 MNSOD 14.7 69.3 10.4 92 11.1
RPL37aC* AL163852 F27H5 N.A. BE577732 13 3 22.7 SGCSNP74 84.6 70.9 10.0 89 11.0
L38 RPL38A III AC002335 T1O24.20 At2g43460 N96748 5 2 18.2 COR15 76.8 78.3 8.1 69 10.7
RPL38B AL138659 T16L24.90 At3g59540 N.F. 0 3 22.4 SNP74 84.6 78.3 8.1 69 10.7
L39 RPL39A* II AC007070 T22F11.20 At2g25210 Z17538 3 2 11.0 g6842 46.7 72.5 6.4 51 12.8
RPL39B* AC009755 F14P3.16 At3g02190 N.F. NE 3 0.4 mi74b 5.8 74.5 6.4 51 12.8
RPL39C* AL021636 F10N7 At4g31981 AV536940 3 4 14.7 g8300 81.2 72.9 6.3 50 12.8
L40 RPL40A III AC006921 F9C22.10 At2g36170 AV533842 4 2 14.4 SGCSNP333 67.97 92.2 14.7 128 10.7
RPL40B AL050300 F22O6.30 At3g52590 Z35369 15 3 19.9 mi456 72.7 92.2 14.7 128 10.7
L41 RPL41A III AC009894 T6H22.15 N.A. AI998257 2 1 3.4 mi3030 83.7 96.0 3.4 25 N.D.
RPL41B* AC002986 YUP8H12R N.A. N.F. 0 1 29.5 SNP253 120.4 iORF
RPL41C* AC018721 T7M7 N.A. N.F. 0 2 17.0 SNP241 74.4 96.0 3.4 25 N.D.
RPL41D AC074395 T8G24.5 At3g08520 N.F. 0 3 2.5 SNP192 11 96.0 3.4 25 N.D.
RPL41E AC009991 F9F8.7 At3g11120 N.F. 0 3 3.4 SNP11 14.7 96.0 3.4 25 N.D.
RPL41F* AC024128 MGH6 N.A. T41975 3 3 4.1 nga162 20.5 96.0 3.4 25 N.D.
RPL41G AL163832 F27K19.200 At3g56020 AI998878 1 3 21.2 SNP189 77.2 96.0 3.4 25 N.D.

Ribosomal protein type corresponding to rat nomenclature. Asterisk, Gene and gene family member designation and genes that were not annotated or incorrectly annotated. NA, Standard AGI gene name and genes that have not been annotated. Classification based on evolutionary group (Group I, represented in eubacteria, archaebacteria, and eukaryotes; Group II, represented in archaebacteria and eukaryotes; and Group III, represented in eukaryotes only). GenBank accession no. corresponding to genomic sequence. BAC clone and position of annotated gene corresponding to genomic sequence. NF, Representative EST or cDNA GenBank accession no. and genes with no corresponding EST are indicated none found. No. of ESTs present in GenBank release 65.0, 0 if no EST is identified, NE if no expression is detected by RT-PCR, and E if expression is detected by RT-PCR. Chromosomal location, AGI map position (Mbp), nearest genetic marker as determined from the AGI map and AGI map position of nearest genetic marker (cM). Percent identity to the rat orthologue determined by the BESTFIT algorithm. iORF, Incomplete open reading frame. Predicted molecular mass (kDa), no. of amino acids of deduced ORF (A.A.), and predicted pI.

Arabidopsis Cytoplasmic r-Proteins Are Encoded by Small Gene Families

We identified multiple Arabidopsis r-protein genes for all 79 r-protein types of rat. We propose a unifying r-protein gene nomenclature in which Arabidopsis r-protein gene names contain the prefix RP (r-protein) and the suffix S or L referring to r-protein type (small or large) modeling that found for the mammalian nomenclature. For example, RPL3 encodes r-protein L3. The one exception to this rule is the conventional nomenclature for the acidic ribosomal phosphoproteins, known as the P proteins (here, RPP2 encodes P2). For each distinct gene family member a letter is provided (i.e. RPL3A and RPL3B are distinct genes that encode L3). This alphabetic designation of gene family members is ordered by chromosomal location. In addition, previously published gene designations are included in Table I in parentheses. The number of genes within an r-protein gene family varies between two and seven (L41), with most families containing three or four genes (Table I and Fig. 1). In 21 instances, the genomic sequences lacked a complete ORF (for example, the deduced ORF encoded a truncated protein due to a premature translational stop codon, a frameshift in the ORF, or an internal deletion) and these were designated an incomplete ORF; in most of these cases (19), there was no cognate EST identified for these presumed pseudogenes. The copy number of r-protein genes is apparently random. There was no bias based on ribosomal subunit or r-protein group classification (see Table I).

Figure 1.

Figure 1

Genomic location of Arabidopsis r-protein genes. The 249 Arabidopsis r-protein genes are mapped by distance (centiMorgans) to nearest genetic marker from the distal short arm on the genetic map of each chromosome (Lister et al., 1993). Centromeres are shown as black circles. Genes listed linearly are tandemly arranged on the same chromosome and those located on the same BAC clone are depicted in red. An asterisk indicates genes with an incomplete ORF. Duplicated regions corresponding to numbers 1, 2, 3, 4, 5, 6, and 7 from Table III are indicated in yellow, red, blue, green, pink, gray, and white, respectively. Genes conserved between duplicated regions are underlined.   (Continued from p. 400)

Arabidopsis r-Protein Genes Are Not Distributed Randomly

Database mining allowed us to identify bacterial artificial chromosome (BAC) or phage artificial chromosome (P1) clones carrying one or several genes for r-proteins (Table I). In addition, existing knowledge of the location of these clones allowed us to identify the positions of the r-protein genes on the AGI map (http://www.Arabidopsis.org). A composite map of the 249 r-protein genes, integrating genomic sequence information and nearest genetic marker data available through AGI, was constructed (Fig. 1). Chromosome map positions are given in centiMorgans from the top of the chromosome, and the nearest genetic marker to each r-protein gene is indicated in Table I. Mapping results are also summarized in Table II. We observed differences in the number of genes per chromosome as the number of r-protein genes located on chromosomes 1, 2, 3, 4, and 5 are 54, 45, 71, 29, and 50, respectively. The distribution of the r-protein genes is visible on the gene map (Fig. 1; r-protein gene density is 538 Kb per r-protein gene for chromosome 1, 436 Kb per r-protein gene for chromosome 2, 326 Kb per r-protein gene for chromosome 3, 605 Kb per r-protein gene for chromosome 4, and 519 Kb per r-protein gene for chromosome 5. This situation appears to contrast with the even distribution of all protein coding sequences observed for the five chromosomes (AGI, 2000); however, statistical analysis (g test, P value = 0.4522) indicated that these differences are not significant. If the r-protein genes were randomly distributed, approximately one gene per 500 kb would be expected; however, in 29 instances, two to four r-protein genes were found on a single BAC (Table II). In eight instances, genes that encode different r-proteins are within 5 kb. In several additional cases, r-protein genes have been duplicated and found on the same BAC, and in one instance the genes are triplicated within the same BAC (S15 on chromosome 5). In addition, there are several examples where only one r-protein gene is found within a BAC; nevertheless, the density of r-protein genes within that region may still be rather high (Fig. 1). These data indicate that localized duplication of these genes has occurred infrequently.

Table II.

Arabidopsis BAC clones containing more than one r-protein gene

Chromosome No. BAC Clone Genes Intergene Distance
Kb
1 F19P19 RPL23A,RPS15A 73.2
F22D16 RPL22A,RPL19A 15.7
F14J9 RPL21A,RPL21B 44.3
F11F8 RPL35A,RPS23A 49.3
T9L6 RPL9B,RPL9C 11.1
T2P11 RPL34A,RPL10B 5.0
F2P9 RPL6B,RPL6C 1.2
2 F6F22 RPS15aB,RPL28A 0.3
RPL28A,RPL31A 0.3
RPL31A,RPS30A 0.6
F15K20 RPP2B,RPP2A 0.7
F9C22 RPS14A,RPL40A 1.0
F12L6 RPL35B,RPL23aA 23.2
T2P4 RPS26A,RPS26B 15.5
3 F3E22 RPL29A,RPL29B 2.6
T9J14 RPS3aA,RPS24A 29.4
F18C1 RPL18B,RPL22B 6.2
F9F8 RPL37aB,RPL41E 56.5
T15B3 RPS29A,RPS29B 20.9
T2J13 RPL13B,RPL13C 15.5
F22O6 RPS14C,RPL40B 0.9
T20K12 RPS27B,RPS27C 0.6
4 F14M19 RPS10A,RPP3A 50.8
F19B15 RPS30B,RPL28C 2.5
F17I5 RPS29C,RPS29D 14.5
5 T22P11 RPL35D,RPL36C 53.2
F9G14 RPS23B,RPL4D 3.2
T5E8 RPS15B,RPS15C 0.8
RPS15C,RPS15D 1.6
MRO11 RPS11C,RPL13D 54.8
T1G16 RPS21C,RPL22C 28.1
MIK19 RPS30C,RPL31C 8.0

In the analysis of the distribution of r-protein genes, we observed that RPL28A and RPS30A are on chromosome 2 and RPL28C and RPS30B are on chromosome 4. This observation led us to compare adjacent genes in these two BACs (Table III, Fig. 1, genes conserved between duplications are underlined; about one-half of the 249 r-protein genes are in currently identified duplicated regions; in Fig. 1, large duplicated regions are shown). However, the percentage of genes encoding the same type of r-protein found in conserved positions in both copies of the duplicated regions is 25% to 30% with a range between 0% to 66% (Table III). This observation is consistent with another study that found only 28% of genes in duplicated regions are actually present in duplicate copies (Vision et al., 2000). The most extreme situation is illustrated by two duplicated segments on chromosomes 1 (6.1–10.8 cM) and 2 (50.6–63.9 cM), which contain two and seven r-protein genes, respectively, of which none are paralogous (Table III, Duplicated Region 2; Fig. 1, red colored regions). In summary, analysis of the distribution of the r-protein genes in the Arabidopsis genome showed no evident clustering of these genes. However, r-protein gene density in some regions of the Arabidopsis genome is much higher than that expected for a uniform distribution.

Table III.

Large duplicated regions of the Arabidopsis genome-containing r-protein genes

Duplicate No. Duplicated Regions
No. of Genes within Duplicated Regions No. of Genes Conserved between Duplicated Regions % Genes Conserved between Duplicated Regions
Chromosome Border BAC clones Position
cM
1 1 F20D23-T7N9 23.6–41.1 6 3 50
1 T6C23-F18B13 110.7–123.8 8 38
2 1 F19P19-F22O13 6.1–10.8 2 0 0
2 T22O13-F4P9 50.6–63.9 7 0
3 2 F16F14-T19L18 30.9–50.6 10 6 60
4 T13J8-T5J17 76.8–108.5 12 50
4 1 F27J15-T6H22 73.5–83.8 3 2 66
3 MBK21-MOE17 16.2–28.1 8 25
5 3 T6H20-F24M12 60.5–68.2 7 2 29
5 K19M22-K1L20 113.7–128 8 25
6 4 FCA8-T13K14 57.6–65.4 3 2 66
5 K23L20-MNJ7 94.1–99.4 4 50
7 4 F22K18-T27E11 72.4–76.8 4 3 50
5 K2I5-MJB24 105.4–113.7 4 50

Expression of Arabidopsis r-Protein Genes Appears to Be Differentially Regulated

The occurrence of r-protein gene families raises the question of whether the genes are differentially regulated. The frequency of ESTs available in GenBank (database of expressed sequence tags) has been proposed as a useful tool for preliminary analysis of gene expression (Adams et al., 1995). Despite the limited number of Arabidopsis ESTs (112,500; release 022301, February 2001) available in GenBank, we used this approach to obtain a first assessment of r-protein gene expression. All gene families have at least one EST for at least one gene, but the frequency of ESTs for individual genes varies greatly between different gene family members and gene families. Many r-protein genes (approximately 20%) apparently are very highly expressed, as indicated by the EST number in Table I (10–40 ESTs). The frequency of ESTs observed per gene was variable among genes from the same family. For example, in the P0 gene family, the three genes encode complete ORFs but were represented by 40, 6, and 0 ESTs. On the other hand, in many cases a representative EST was observed for each member of a given family. Cognate ESTs were not found for 52 of the r-protein genes (approximately 20%). Of these, 19 lack a complete ORF and hence are most likely pseudogenes. Genes with a complete deduced ORF may lack a representative EST due to low levels of mRNA accumulation solely in specific cell types or at a specific developmental stage. To examine this possibility, PCR and RT-PCR (with gene specific primers) using a cDNA library or RNA prepared from 3-week-old plants was performed on a subset of r-protein genes lacking a corresponding EST. A PCR (or RT-PCR) product was observed for many (72%) of these genes (data not shown), suggesting that they may be transcribed at some stage in development. Consistent with analyses from other groups, we observed differential levels of expression of individual gene family members.

Global analysis of the expression of the 54, 45, 71, 29, and 50 r-protein genes located on chromosomes 1, 2, 3, 4, and 5, respectively, showed that the percentage of these r-protein genes for which an EST is available is 74.1%, 80%, 77.4%, 79.3%, and 84%, respectively. The average numbers of ESTs per mapped r-protein gene per chromosome are 7.8, 5.3, 5.4, 5.3, and 6.1 (chromosomes 1, 2, 3, 4, and 5, respectively). These results suggest a positive bias in favor of chromosome 1 and 5: The r-protein genes on the two chromosomes, in average, seemed to be more abundantly expressed. However, statistical analysis using a non-parametric ANOVA (Kruskal-Wallis test, performed because the data failed to meet the assumption of normality [data not shown] for a standard ANOVA) indicates that there is no significant difference (P value = 0.6087) in the expression of the r-protein genes, among the five chromosomes, based on EST frequency (SAS Institute Inc., 1989).

Biochemical Characteristics of Deduced Arabidopsis r-Proteins

The deduced amino acid sequence for each of the 80 types of r-proteins was determined. In addition, for each r-protein, the predicted molecular mass and pI was calculated, and the percent identity to the rat ortholgue was determined. The deduced Arabidopsis r-proteins range in size from 44.7 (L4) to 3.4 (L31) kD. Of the deduced proteins, Sa, P0, P1, P2, P3, and S12 were acidic (pI 4.0–5.8) and the remainder were basic, ranging in pI from 8.1 (S27) to 12.8 (S30 and L39). The positive charge of the majority of r-proteins is consistent with their interaction with rRNA. The identity between Arabidopsis and rat orthologues averaged 66% and ranged from 96% for L41% to 35% for L28. It is interesting that an L28 orthologue was not identified in the genomic sequence of S. cerevisiae (Planta and Mager, 1998), indicating that it is a rather divergent r-protein. A final observation was that the identity between rat and individual Arabidopsis orthologues (deduced proteins from the same gene family) were usually within 0% to 5.0% of one another, indicating that members of individual r-protein families are highly conserved. However, there were a few exceptions where the identities within an r-protein family varied 14.1%, 24.0%, and 30.1%, corresponding to the r-proteins P2, L7, and S15a, respectively. These distinctions in proteins encoded by these classes could result in ribosomal heterogeneity or may reflect the evolution of proteins with extra-ribosomal function.

DISCUSSION

Arabidopsis Ribosomes Contain at Least 80 r-Protein Types, Encoded by 249 Genes

Previous work from our two groups identified 106 Arabidopsis r-protein genes by contig construction from EST sequences coding for 50 orthologues of yeast r-proteins (Cooke et al., 1996) and 77 Arabidopsis orthologues of rat r-proteins (Bailey-Serres, 1998). This report extends the parallel analyses of our two groups on the set of Arabidopsis r-proteins that can be defined by homology to the 79 known eukaryotic r-proteins. All rat r-protein genes have an orthologue in Arabidopsis; however, plants possess an additional r-protein, P3, that appears to be limited to the plant kingdom (Szick et al., 1998). A total of 80 r-protein types encoded by 249 genes were classified, positioned on the AGI map, and the nearest genetic marker identified. Based on this study, Arabidopsis has at least 32 small ribosomal subunit proteins encoded by 101 genes and 48 large ribosomal subunit proteins encoded by 148 genes. Due to the extensive segmental duplication of the Arabidopsis genome, all r-protein genes have between two and several paralogues. Our study included analysis of genomic sequences and ESTs encoding r-proteins. Because all ESTs were assigned to specific genomic sequences, it is unlikely that additional genes that encode rat r-protein orthologues will be identified in the unsequenced centromeric and rDNA regions. Based on this analysis of Arabidopsis r-protein genes, the protein composition of plant ribosomes is very similar to that of other eukaryotes. Our study provides an entry to several important issues such as systematic annotation of r-protein genes; normalization of nomenclature; evolutionary studies of gene structure; analysis of gene expression at the transcriptional, posttranscriptional, and translational levels; examination of r-protein transport to the nucleolus; and ribosome biogenesis.

Analysis of Arabidopsis r-Protein Gene Distribution Provides Insight into r-Protein Gene Evolution

In humans, r-protein genes are found on all chromosomes but with a bias toward chromosome 19 (Kenmochi et al., 1998b). In prokaryotic genomes, r-protein gene clustering is found in the form of operons in which expression of several genes is coordinately regulated under a single promoter (Nomura et al., 1984). No obvious similar clustering has been reported in eukaryotic genomes and recent results (Kenmochi et al., 1998a) showed only one example of local clustering in the human genome, three genes encoding L13A, S11, and L18 being located within 0.6 cM. It is noteworthy that in the Arabidopsis genome, r-protein gene density is much higher in several regions than would be expected from a uniform distribution. For example, the chromosome 2 BAC clone F6F22 contains four different r-protein gene types within 1.2 kb (Table II). Whether this grouping corresponds to a fossil functional clustering remains to be established by the analysis of different plant genomes.

Analysis of r-protein gene organization has served as a starting point for new insights on genome organization and dynamics in Arabidopsis. It has become obvious that the Arabidopsis genome is a mosaic of duplicated regions (AGI, 2000; Blanc et al., 2000; Paterson et al., 2000; Vision et al., 2000). These data have extended observations made by comparison of chromosomes 2 and 4 (Lin et al., 1999; Mayer et al., 1999). These duplications are either the result of reciprocal translocations between Arabidopsis chromosomes or of an ancient polyploidisation event. It can be reasonably assumed that large duplications constitute one of the main factors of gene duplication in Arabidopsis and have certainly contributed to the increase in r-protein gene number because one-half of the 249 mapped genes are located in duplicated regions. However, closer examination of r-protein genes in duplicated regions shows that considerable rearrangements involving r-protein genes have taken place following duplication of chromosomal segments. Genes encoding the same r-protein are found in conserved positions in both duplicated segments for only approximately 25% of the genes. This observation indicates that although many r-protein genes occur in large duplicated segments, the story is much more complex. It appears that one copy frequently was lost for many of the pairs following duplication of a large chromosomal region, or r-protein genes have been inserted following duplication events. However, the relatively low number of intron-less genes having an intron-containing paralogue argues against the latter mechanism (Martinez et al., 1989).

Because r-proteins form a complex macromolecule in which coordinated regulation of protein levels as well as steric constraints are essential, it is possible that negative selection has led to the elimination of duplicated copies of certain genes. However, the Group I class of r-proteins are found to occur within eubacteria, archaebacteria, and eukaryotes (Wool et al., 1995), yet do not show any bias toward lower copy number than Group II and III r-proteins. Our analysis has shown in addition that tandem duplication, which is another mechanism to increase gene copy number, does not appear to have been important in the expansion of r-protein gene families. Because Arabidopsis is a model genome that will be used to investigate the genomes of many cultivated crops, and because r-protein genes have been conserved throughout evolution, this work should serve as a basis to analyze the distribution and expression of r-protein genes in crop plant species.

The Majority of Arabidopsis r-Protein Genes Appear to Be Expressed

An important question raised by the occurrence of multigene families is the regulation and level of expression of each member in the family. Assessing r-protein gene expression by the presence of an EST showed that at least 77% of r-protein genes (not including the 21 genes with incomplete ORFs) are expressed at a level detectable by an EST. Most or all copies of genes in the individual families have been tagged. The r-protein genes for which no EST is yet available could correspond either to genes that are rarely transcribed or to pseudogenes. As shown in Table I, several r-protein genes for which an EST was not identified have truncated ORFs or deletions within their ORFs. Analysis of expression, PCR, or RT-PCR indicated that many of these genes are in fact expressed (Table I, EST column, represented with an E or NE). Only 7% of r-protein genes were not expressed in the tissues tested. The infrequent nature (7%) of potential r-protein pseudogenes is in agreement with previous data of Lin et al. (1999), who reported that only 10% of all the genes identified or predicted on chromosome 2 correspond to pseudogenes. Our observation that the majority of r-protein genes are expressed in plants is notably different from the situation reported in mammals, in which multiple pseudogenes and only one functional, intron-containing gene was observed for most r-proteins (Wiedemann and Perry, 1984; Wagner and Perry, 1985; Baker and Board, 1992).

The large number of expressed genes in multigene families in plants is probably due to the fact that plants have evolved by polyploidy (Dornelas et al., 1998), followed by specialization of the function or expression patterns of gene family members, thus allowing increased plasticity in response to non-optimal growth conditions. The high degree of sequence identity between different r-proteins suggests specialization by different temporal or spatial expression patterns to increase protein synthesis at certain developmental times. To date, all detailed analyses of Arabidopsis r-protein genes have illustrated distinctions in regulation of expression of gene family members. For example, high levels of expression of one Arabidopsis L11 gene (RPL11C, previously called RPL16B) was observed in shoot and primary root meristems and lateral root primordia in response to auxin treatment, whereas expression of another L11 gene (RPL11A, previously called RPL16A) showed more cell type-specific gene expression (Williams and Sussex, 1995). Mutations in Arabidopsis S13 and S18 genes were shown to cause a pointed first leaf (pfl) phenotype, remarkably indicating that mutations that alter the expression of r-protein genes may confer a similar phenotype (Van Lijsebettens et al., 1994; Ito et al., 2000). In pfl1, a T-DNA insertion into the S18A (RPS18A) gene results in complete abrogation of gene expression (Van Lijsebettens et al., 1994). Although S18 is encoded by three genes that appear to have overlapping expression, synthesis in mitotically active tissues seems to be required for normal leaf development. In pfl2, caused by a Ds insertion into the S13A (RPS13B) gene, a significantly reduced number and increased size of subepidermal palisade cells of the first leaf was observed (Ito et al., 2000). Consistent with the apparent effects on cell division, a conditional deletion of r-protein S6 gene in mice does not impair the growth of liver cells following partial hepatectomy but does block the progression through the cell cycle (Volarevic et al., 2000). In this example, existing levels of ribosomes are sufficient for cell growth. In contrast, r-protein gene mutations in Drosophila melanogaster are known to cause the haploinsufficient Minute phenotype that shows slower rates of cell growth and division (Lambertsson, 1998). Further studies using DNA microarray studies, r-protein gene promoter fusions to a reporter gene, and r-protein gene mutants will be necessary to assess the regulation and role of individual r-protein genes. These studies hopefully will shed light on the role of r-proteins and ribosome biogenesis on regulation of cell growth and proliferation in plants.

Our results show varying numbers of r-protein genes in different families, although it is clear that control mechanisms must exist to ensure the presence of stoichiometric levels of each protein in the ribosomes. This could be achieved by higher expression levels of members of smaller gene families. However, expression levels of different members deduced from the number of cognate ESTs show no clear inverse relationship between the level of expression and the number of genes. Therefore, it is likely that r-protein synthesis is also controlled at a posttranscriptional step. It has been determined that vertebrate r-protein levels are regulated at the translational level, possibly by sequences around a polypyrimidine tract present at the 5′ end of the mRNA, through the regulation of r-protein S6 phosphorylation (Fumagalli and Thomas, 2000; Meyuhas, 2000; Meyuhas and Hornstein, 2000). In plants, posttranscriptional regulation of rapeseed L13 r-protein (Sáez-Vásquez et al., 2000), maize P2a (Fennoy et al., 1998), and maize S6 (Sanchez de Jimenez et al., 1999) expression was reported. Preliminary surveys suggest that a number of plant r-protein mRNAs possess 5′-polypyrimidine tracts (A. Williams and J. Bailey-Serres, unpublished data). In addition, studies with a cell-free wheat germ translation system confirmed that translation of an mRNA with a 5′-polypyrimidine tract was regulated by levels of a titratable repressor protein (Shama and Meyuhas, 1996). Furthermore, the phosphorylation of r-protein S6 is regulated in plants (Turck et al., 1998; A. Williams and J. Bailey-Serres, unpublished data). These observations indicate that the role of translational regulation in r-protein synthesis needs to be rigorously examined.

The existence of differentially regulated multigene families encoding r-proteins raises the additional possibility of ribosomal heterogeneity and its possible functional significance. Here, we observed that the frequency of ESTs for different r-protein gene family members is variable (Table I). Szick-Miranda and Bailey-Serres (2001) recently demonstrated developmentally and environmentally regulated heterogeneity of the composition of the P2-type of r-protein in ribosomes of maize. This, along with our results, raises the intriguing possibility that microheterogeneity in the protein composition of ribosomes may occur at the tissue or cellular level. Such heterogeneity might be used for fine tuning of the efficiency of the translational machinery during development or under specific growth conditions.

In conclusion, this work reports a number of original findings: (a) 249 r-protein genes encoding 79 rat orthologues, and one plant-specific r-protein (P3), were identified and mapped in Arabidopsis; (b) the analysis revealed that r-protein genes are distributed over all Arabidopsis chromosomes; (c) the examination of frequency of ESTs for the different r-proteins gene family members and RT-PCR analysis of a several r-protein genes families demonstrated differential patterns of gene expression with no clear relationship between expression levels and gene number; (d) the expression analysis utilizing the number of ESTs suggest that there is no significant bias in the expression of the r-protein genes among the five chromosomes; and (e) large duplications of chromosomal segments have contributed to the increase in gene copy number but is insufficient to account for all copies because it seems that many duplicated genes have been eliminated during evolution. The identification of the r-protein genes and the determination of their primary structure and organization constitutes a first step to determine their biological role, mechanisms controlling their expression, and modeling of ribosome structure and function in plants.

MATERIALS AND METHODS

Identification and Mapping of ESTs Corresponding to r-Protein Genes

The 79 rat (Rattus norvegicus) r-protein sequences were obtained from Swiss-PROT (Bairoch and Apweiler, 2000) and the corresponding Arabidopsis ESTs were identified by TBLASTN alignment (Altschul et al., 1997) against all Arabidopsis sequences available in the database of expressed sequence tags and GenBank (http://www.ncbi.nlm.nih.gov). Sequences whose putative translation product showed significant similarity to the rat sequence were collected using the Query server at NCBI (http://www.ncbi.nlm.nih.gov/GenBank/GenBankEmail.html), imported into Sequencher (Gene Codes Corp. Ann Arbor, MI), trimmed at the 3′ end to remove ambiguous sequences, and contigs were constructed with 90% identity in 30-nucleotide steps. Assembled contigs were manually adjusted to identify members of the same gene family as described by Cooke et al. (1997). ESTs were also compared with genomic sequences to confirm identity. From this analysis, the minimal number of genes expressed in each r-protein gene family was determined. The sequence of each identified contig is available on request.

At the beginning of this work, the easiest strategy to map available EST contigs was by PCR on yeast artificial chromosome (YAC) DNA pools using gene-specific primers (Camilleri et al., 1998). Because most of the YACs in the library have been progressively anchored with respect to the genetic map (Lister and Dean, 1993), positioning of an EST on a YAC immediately gave an approximate map position.

Identification of r-Protein Genes and Mapping by Genomic Sequencing

Arabidopsis r-protein genes were identified in the genomic sequence using the same approach as for ESTs using TBLASTN of rat r-proteins against Arabidopsis genomic sequences. Despite the fact that gene annotation lagged behind sequencing, it became easiest to retrieve r-protein genes from the genomic sequence. Careful attention was paid to identify gene exons based on perfect match to ESTs (so that the same gene was not counted twice). Genes encoding plastidic or mitochondrial r-proteins were frequently identified by similarity to known chloroplast or mitochondiral proteins. These genes usually possessed targeting sequences and had higher identity to Escherichia coli r-protein genes than those of rat, and were excluded. Identification of a gene by genomic sequence mining allowed for positioning the gene on the AGI map. The percent identity to rat r-protein genes was determined by BESTFIT algorithm available through GCG (University of Wisconsin Genetics Computer Group, Madison, WI). The predicted molecular mass and pI of deduced r-proteins was determined by use of PEPTIDESORT (University of Wisconsin Genetics Computer Group). Genes that were not annotated or were annotated incorrectly were translated using MBS Translator (available at http://mbshortcuts.com/translator/) and intron/exon boundaries were determined by visual inspection of translated sequences comparing genes within a given family that were correctly annotated.

Expression Analysis of r-Protein Genes

Expression levels were estimated based on the number of ESTs in contigs, constructed as described by Cooke et al. (1997), corresponding to individual r-protein genes. Expression analysis of r-protein genes lacking a corresponding EST was examined using PCR or RT-PCR, with gene-specific primers. PCR analysis was performed on an Arabidopsis cDNA library (Newman et al., 1994). RT-PCR was performed on RNA extracted from 3-week-old Arabidopsis ecotype Col 0 plants. Total RNA extraction was performed as previously described (Raynal et al., 1999). Amplification products were resolved on agarose gels and visualized by staining with ethidium bromide. Specific primers for Arabidopsis r-protein genes were designed using regions presenting a sequence polymorphism. Primer sequences are available on request.

ACKNOWLEDGMENTS

We thank the Arabidopsis Biological Resource Center (Ohio State University, Columbus) for the gift of ESTs, and Mike Bryant (Department of Biology, University of California, Riverside) for his expert assistance with the statistical analysis. We gratefully acknowledge all our colleagues from the AGI consortium for their immediate release of sequence data. Without this policy, such work would not have been possible.

Footnotes

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.).

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.010265.

LITERATURE CITED

  1. Adams MD, Kerlavage RD, Fleischmann RA, Fuldner CJ, Bult NH, Lee EF, Kirkness KG, Weinstock JD, Gocayne O, White Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature. 1995;377:3–17. [PubMed] [Google Scholar]
  2. AGI. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
  3. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Asamizu E, Nakamura Y, Sato S, Tabata S. A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries. DNA Res. 2000;7:175–180. doi: 10.1093/dnares/7.3.175. [DOI] [PubMed] [Google Scholar]
  5. Bailey-Serres J. Cytoplasmic ribosomes of higher plants. In: Bailey-Serres J, Gallie D, editors. A Look Beyond Transcriptionii: Mechanisms Determining mRNA Stability and Translation in Plants. Rockville, MD: American Society of Plant Physiologists; 1998. pp. 125–144. [Google Scholar]
  6. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000;28:45–48. doi: 10.1093/nar/28.1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Baker RT, Board PG. The human ubiquitin/52-residue ribosomal protein fusion gene subfamily (UbA52) is composed primarily of processed pseudogenes. Genomics. 1992;14:520–522. doi: 10.1016/s0888-7543(05)80258-7. [DOI] [PubMed] [Google Scholar]
  8. Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature. 1999;400:841–846. doi: 10.1038/23641. [DOI] [PubMed] [Google Scholar]
  9. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000;289:905–920. doi: 10.1126/science.289.5481.905. [DOI] [PubMed] [Google Scholar]
  10. Beltran-Pena E, Ortiz-Lopez A, Sanchez de Jimenez E. Synthesis of ribosomal proteins from stored mRNAs early in seed germination. Plant Mol Biol. 1995;28:327–336. doi: 10.1007/BF00020251. [DOI] [PubMed] [Google Scholar]
  11. Bevan M, Ecker J, Theologis S, Federspiel N, Davis R, McCombie D, Martienssen R, Chen E, Waterston B, Wilson R. Objective: the complete sequence of a plant genome. Plant Cell. 1997;9:476–478. doi: 10.1105/tpc.9.4.476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M. Extensive duplication and reshuffling in the Arabidopsis thaliana genome. Plant Cell. 2000;12:1095–1101. doi: 10.1105/tpc.12.7.1093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Camilleri CJ, Lafleuriel C, Macadre F, Varoquaux Y, Parmentier G, Picard M, Caboche M, Bouchez D. A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J. 1998;14:633–642. doi: 10.1046/j.1365-313x.1998.00159.x. [DOI] [PubMed] [Google Scholar]
  14. Clemons WM, May JL, Jr, Wimberly BT, McCutcheon JP, Capel MS, Ramakrishnan V. Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature. 1999;400:833–840. doi: 10.1038/23631. [DOI] [PubMed] [Google Scholar]
  15. Cooke R, Raynal M, Laudié M, Delseny M. Identification of members of gene families in Arabidopsis thaliana by contig constructions from partial cDNA sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J. 1997;11:1127–1140. doi: 10.1046/j.1365-313x.1997.11051127.x. [DOI] [PubMed] [Google Scholar]
  16. Cooke R, Raynal M, Laudie M, Grellet F, Delseny M, Morris PC, Guerrier D, Giraudat J, Quigley F, Clabault G. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J. 1996;9:101–124. doi: 10.1046/j.1365-313x.1996.09010101.x. [DOI] [PubMed] [Google Scholar]
  17. Culver GM, Cate JH, Yusupova GZ, Yusupov MM, Noller HF. Identification of an RNA-protein bridge spanning the ribosomal subunit interface. Science. 1999;285:2133–2136. doi: 10.1126/science.285.5436.2133. [DOI] [PubMed] [Google Scholar]
  18. Dornelas MC, Lejeune B, Dron M, Kreis M. The Arabidopsis SHAGGY-related protein kinase (ASK gene family: structure organization and evolution) Gene. 1998;212:249–257. doi: 10.1016/s0378-1119(98)00147-4. [DOI] [PubMed] [Google Scholar]
  19. Dresselhaus T, Cordts S, Heuer S, Sauter M, Lorz H, Kranz E. Novel ribosomal genes from maize are differentially expressed in the zygotic and somatic cell cycles. Mol Gen Genet. 1999;261:416–427. doi: 10.1007/s004380050983. [DOI] [PubMed] [Google Scholar]
  20. Fennoy SL, Nong T, Bailey-Serres J. Transcriptional and post-transcriptional processes regulate gene expression in oxygen-deprived roots of maize. Plant J. 1998;15:727–735. doi: 10.1046/j.1365-313X.1998.00249.x. [DOI] [PubMed] [Google Scholar]
  21. Fumagalli S, Thomas G. S6 phosphorylation and signal transduction. In: Sonenberg N, Hershey JWB, Mathews MB, editors. Translational Control of Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Press; 2000. pp. 695–717. [Google Scholar]
  22. Gantt JS, Key JL. Auxin-induced changes in the level of translatable ribosomal protein messenger ribonucleic acids in soybean hypocotyl. Biochemistry. 1983;22:4131–4139. [Google Scholar]
  23. Gantt JS, Key JL. Coordinate expression of ribosomal protein mRNAs following auxin treatment of soybean hypocotyls. J Biol Chem. 1985;260:6175–81. [PubMed] [Google Scholar]
  24. Garo J, Kim SR, Chung YY, Lee JM, An G. Developmental and environmental regulation of two ribosomal protein genes in tobacco. Plant Mol Biol. 1994;25:761–770. doi: 10.1007/BF00028872. [DOI] [PubMed] [Google Scholar]
  25. Graack HR, Wittmann-Liebold B. Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J. 1998;329:433–448. doi: 10.1042/bj3290433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M. Life with 6000 genes. Science. 1996;274:546–567. doi: 10.1126/science.274.5287.546. [DOI] [PubMed] [Google Scholar]
  27. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J. 1993;4:1051–1061. doi: 10.1046/j.1365-313x.1993.04061051.x. [DOI] [PubMed] [Google Scholar]
  28. Ito T, Kim GT, Shinozaki K. Disruption of an Arabidopsis cytoplasmic ribosomal protein S13-homologous gene by transposon-mediated mutagenesis causes aberrant growth and development. Plant J. 2000;22:257–64. doi: 10.1046/j.1365-313x.2000.00728.x. [DOI] [PubMed] [Google Scholar]
  29. Joanin P, Gigot C, Phillips G. cDNA nucleotide sequence and expression of a maize cytoplasmic ribosomal protein S13 gene. Plant Mol Biol. 1993;21:701–704. doi: 10.1007/BF00014553. [DOI] [PubMed] [Google Scholar]
  30. Kenmochi N, Ashworth LK, Lennon G, Higa S, Tanaka T. High-resolution mapping of ribosomal protein genes to human chromosome 19. Genome Res. 1998b;5:229–233. doi: 10.1093/dnares/5.4.229. [DOI] [PubMed] [Google Scholar]
  31. Kenmochi N, Kawaguchi T, Rozen S, Davis E, Goodman N, Hudson TJ, Tanaka T, Page DC. A map of 75 human ribosomal protein genes. Genome Res. 1998a;8:509–523. doi: 10.1101/gr.8.5.509. [DOI] [PubMed] [Google Scholar]
  32. Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL. A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J Biol Chem. 2000;275:32585–32591. doi: 10.1074/jbc.M003596200. [DOI] [PubMed] [Google Scholar]
  33. Lambertsson A. The minute genes in Drosophila and their molecular functions. Adv Genet. 1998;38:69–134. doi: 10.1016/s0065-2660(08)60142-x. [DOI] [PubMed] [Google Scholar]
  34. Larkin JC, Hunsperger JP, Culley D, Rubenstein I, Siflow CD. The organization and expression of maize ribosomal protein gene family. Genes Dev. 1989;3:500–509. doi: 10.1101/gad.3.4.500. [DOI] [PubMed] [Google Scholar]
  35. Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 1999;402:761–768. doi: 10.1038/45471. [DOI] [PubMed] [Google Scholar]
  36. Lister C, Dean D. Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 1993;4:745–750. doi: 10.1046/j.1365-313x.1996.10040733.x. [DOI] [PubMed] [Google Scholar]
  37. Martinez P, Martin W, Cerff R. Structure, evolution and anaerobic regulation of a nuclear gene encoding cytosolic glyceraldehyde 3-phosphate dehydrogenase from maize. J Mol Biol. 1989;208:551–565. doi: 10.1016/0022-2836(89)90147-2. [DOI] [PubMed] [Google Scholar]
  38. Matheson AT, Auer J, Ramíerez C, Böck A. Structure and evolution of archaebacterial ribosomal proteins. In: Hill WE, Dahlberg A, Garrett RE, Moore PB, Schlessinger D, Warner, editors. , The Ribosome, Structure, Function and Evolution. Washington, DC: American Society of Microbiologists; 1990. pp. 617–633. [Google Scholar]
  39. Mayer K, Schuller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999;402:769–777. doi: 10.1038/47134. [DOI] [PubMed] [Google Scholar]
  40. Meyuhas O. Synthesis of the translational apparatus is regulated at the translational level. Eur J Biochem. 2000;267:6321–6330. doi: 10.1046/j.1432-1327.2000.01719.x. [DOI] [PubMed] [Google Scholar]
  41. Meyuhas O, Hornstein E. Translational control of TOP mRNAs. In: Sonenberg N, Hershey JWB, Mathews MB, editors. Translational Control of Gene Expression. Cold Spring Harbor, NY: Cold Spring Harbor Press, eds; 2000. pp. 671–693. [Google Scholar]
  42. Newman T, Debruijn FJ, Green P, Keegstra K, Kende H, McIntosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 1994;106:1241–1255. doi: 10.1104/pp.106.4.1241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Nomura M, Gourse R, Banghman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem. 1984;53:75–117. doi: 10.1146/annurev.bi.53.070184.000451. [DOI] [PubMed] [Google Scholar]
  44. Planta RJ, Mager WH. The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Yeast. 1998;14:471–477. doi: 10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U. [DOI] [PubMed] [Google Scholar]
  45. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming R. Comparative genomics of plant chromosomes. Plant Cell. 2000;12:1523–40. doi: 10.1105/tpc.12.9.1523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Raynal M, Guilleminot J, Gueguen C, Cooke R, Delseny M, Gruber V. Structure, organization and expression of two closely related novel Lea (late-embryogenesis-abundant) genes in Arabidopsis thaliana. Plant Mol Biol. 1999;40:153–165. doi: 10.1023/a:1026403215270. [DOI] [PubMed] [Google Scholar]
  47. Revenkova E, Masson J, Koncz C, Afsar K, Jakovleva L, Paszkowski J. Involvement of Arabidopsis thaliana ribosomal protein S27 in mRNA degradation triggered by genotoxic stress. EMBO J. 1999;18:490–499. doi: 10.1093/emboj/18.2.490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Sáez-Vásquez J, Gallois P, Delseny M. Accumulation and nuclear targeting of BnC24 a Brassica napus ribosomal protein corresponding to a mRNA accumulating in response to cold treatment. Plant Sci. 2000;156:35–46. doi: 10.1016/s0168-9452(00)00229-6. [DOI] [PubMed] [Google Scholar]
  49. SAS Institute Inc. SAS User's Guide: Statistics, Version 6. Ed 4. Vol. 2. Cary, NC: SAS Institute Inc.; 1989. [Google Scholar]
  50. Sanchez de Jimenez E, Aguilar R, Dinkova T. S6 ribosomal protein phosphorylation and translation of stored mRNA in maize. Biochemie. 1999;79:187–194. doi: 10.1016/s0300-9084(97)83505-5. [DOI] [PubMed] [Google Scholar]
  51. Shama S, Meyuhas O. The translational cis-regulatory element of mammalian ribosomal protein mRNAs is recognized by the plant translational apparatus. Eur J Biochem. 1996;236:383–388. doi: 10.1111/j.1432-1033.1996.00383.x. [DOI] [PubMed] [Google Scholar]
  52. Szick K, Springer M, Bailey-Serres J. Evolutionary analyses of the 12-kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes. Proc Natl Acad Sci USA. 1998;95:2378–2383. doi: 10.1073/pnas.95.5.2378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Szick-Miranda K, Bailey-Serres J. Regulated heterogeneity in 12-kDa P-protein phosphorylation and composition of ribosomes in maize (Zea mays L.) J Biol Chem. 2001;276:10921–10928. doi: 10.1074/jbc.M011002200. [DOI] [PubMed] [Google Scholar]
  54. Tsugeki R, Kochieva EZ, Fedoroff NV. A transposon insertion in the Arabidopsis SSR16 gene causes an embryo-defective lethal mutation. Plant J. 1996;10:479–489. doi: 10.1046/j.1365-313x.1996.10030479.x. [DOI] [PubMed] [Google Scholar]
  55. Turck F, Kozma SC, Thomas G, Nagy F. A heat-sensitive Arabidopsis thaliana kinase substitutes for human p70(s6k) function in vivo. Mol Cell Biol. 1998;18:2038–2044. doi: 10.1128/mcb.18.4.2038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Van Lijsebettens M, Vanderhaeghen R, De Block M, Bauw G, Villarroel R, Van Montagu M. An S18 ribosomal protein gene copy at the Arabidopsis PFL locus affects plant development by its specific expression in meristems. EMBO J. 1994;13:3378–3388. doi: 10.1002/j.1460-2075.1994.tb06640.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Veuthey AL, Bittar G. Phylogenetic relationships of fungi Plantae and Animalia inferred from homologous comparison of ribosomal proteins. J Mol Evol. 1998;47:81–92. doi: 10.1007/pl00006365. [DOI] [PubMed] [Google Scholar]
  58. Vision TJ, Brown DG, Tanksley SD. The origins of genomic duplications in Arabidopsis. Science. 2000;290:2114–2117. doi: 10.1126/science.290.5499.2114. [DOI] [PubMed] [Google Scholar]
  59. Volarevic S, Stewart MJ, Ledermann B, Zilberman F, Terracciano L, Montini E, Grompe M, Kozma SC, Thomas G. Proliferation, but not growth, blocked by conditional deletion of 40S ribosomal protein S6. Science. 2000;288:2045–2047. doi: 10.1126/science.288.5473.2045. [DOI] [PubMed] [Google Scholar]
  60. Wagner MM, Perry RP. Characterization of multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene countreparts by an analysis of total genomic. DNA Mol Cell Biol. 1985;5:3560–3576. doi: 10.1128/mcb.5.12.3560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Wiedemann LM, Perry RP. Characterization of expressed gene and several processed pseudogenes for the mouse ribosomal protein gene family. Mol Cell Biol. 1984;4:2518–2528. doi: 10.1128/mcb.4.11.2518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Williams ME, Sussex LM. Developmental regulation of ribosomal protein L16 genes in Arabidopsis thaliana. Plant J. 1995;8:65–76. doi: 10.1046/j.1365-313x.1995.08010065.x. [DOI] [PubMed] [Google Scholar]
  63. Wittmann HG. Components of bacterial ribosomes. Ann Rev Biochem. 1982;51:155–183. doi: 10.1146/annurev.bi.51.070182.001103. [DOI] [PubMed] [Google Scholar]
  64. Wittmann-Leibold B, Kopke AKE, Arndt E, Kromer W, Hatakeyama T, Wittmann H-G. Sequence comparison and evolution of ribosomal proteins and their genes. In: Hill WE, Dahlberg A, Garrett RE, Moore PB, Schlessinger D, Warner JR, editors. The Ribosome, Structure, Function and Evolution. Washington, DC: American Society of Microbiologists; 1990. pp. 598–616. [Google Scholar]
  65. Wool IG, Chan YL, Gluck A. Structure and evolution of mammalian ribosomal proteins. Biochem Cell Biol. 1995;73:933–947. doi: 10.1139/o95-101. [DOI] [PubMed] [Google Scholar]
  66. Wu JW, Matsui E, Yamamoto K, Nagamura Y, Kurata N, Sasaki T, Minobe Y. Genomic organization of 57 ribosomal protein genes in rice (Oryza sativa) through RFLP mapping. Genome. 1995;38:1189–1200. doi: 10.1139/g95-157. [DOI] [PubMed] [Google Scholar]
  67. Yamaguchi K, Subramanian AR. The plastid ribosomal proteins: identification of all the proteins in the 50 S subunit of an organelle ribosome (chloroplast) J Biol Chem. 2000;275:28466–28482. doi: 10.1074/jbc.M005012200. [DOI] [PubMed] [Google Scholar]
  68. Yamaguchi K, von Knoblauch K, Subramanian AR. The plastid ribosomal proteins: identification of all the proteins in the 30 S subunit of an organelle ribosome (chloroplast) J Biol Chem. 2000;275:28455–28465. doi: 10.1074/jbc.M004350200. [DOI] [PubMed] [Google Scholar]
  69. Zinn AR, Ross JL. Turner syndrome and haploinsufficiency. Curr Opin Genet Dev. 1998;8:322–327. doi: 10.1016/s0959-437x(98)80089-0. [DOI] [PubMed] [Google Scholar]

Articles from Plant Physiology are provided here courtesy of Oxford University Press

RESOURCES