The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome

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.

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)