The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes

The ribosome is the cellular organelle responsible for protein synthesis in all cells. Recent analyses of the ribosome's structure using X-ray crystallography have enhanced our understanding of the structural basis of ribosome function (Ban et al. 2000; Schluenzen et al. 2000; Wimberly et al. 2000; Yusupov et al. 2001). In contrast, comparatively little is known about ribosome biogenesis, especially in higher eukaryotes. In mammalian cells, the biogenesis of cytoplasmic ribosomes requires assembly of 4 RNA molecules and 79 different proteins (Wool 1979). With the exception of two proteins, all of these components are present as single copies within the ribosome. Typically, mammalian cells contain ∼4 × 106 cytoplasmic ribosomes, which account for 80% of all cellular RNA and 5%–10% of cellular proteins. Investigation of the mechanism that controls the coordinated expression of these components is a challenge. Three different RNA polymerases are involved in production of these RNAs and proteins, RNA polymerase I (POL I) is involved in production of the 28S, 18S, and 5.8S rRNAs, POL II in production of ribosomal proteins (RPs), and POL III in production of the 5S rRNA. The amino acid sequences of all rat and human RPs have been deduced (Wool et al. 1996), and the nucleotide sequences of thousands of eukaryotic rRNAs are now known (The Ribosome Database Project; Maidak et al. 2001). On the other hand, only a handful of mammalian RP genes have been studied in terms of their genomic structure. Unlike rRNAs, which are encoded by several hundred copies of genes, each mammalian RP is typically encoded by a single gene. Single functional genes generate large numbers of processed pseudogenes (Dudov and Perry 1984; Wagner and Perry 1985; Kuzumaki et al. 1987), which, however has hampered the cloning of the functional genes and, hence, analysis of their genomic structure. Even though some enhancer/promoter sites have been identified (Rhoads et al. 1986; Hariharan et al. 1989; Kenmochi et al. 1992; Toku and Tanaka 1996), we are far from understanding the basis of the coordinated expression of RP genes. Despite the central role played by cytoplasmic ribosomes in organismal growth and development, the effects of their mutation have been largely ignored, particularly with respect to human disease. One might predict that genetic defects in the components of ribosomes would invariably result in early embryonic death. However, there is strong evidence in Drosophila that a quantitative deficiency of any one of the cytoplasmic RPs can yield the viable but abnormal Minute phenotype (Kongsuwan et al. 1985; Lambertsson 1998). Moreover, heterozygous mutations in the ribosomal protein S19 gene (RPS19) have been found in a subset of patients with Diamond-Blackfan anemia (Draptchinskaia et al. 1999; Willig et al. 1999), a rare form of chronic anemia characterized by the absence or low levels of erythroid precursors in the bone marrow (Diamond et al. 1976; Halperin et al. 1989). It has been suggested that RPS4, encoded by both the X and Y chromosomes, is an important factor for Turner syndrome (Fisher et al. 1990; Watanabe et al. 1993), a complex human phenotype associated with monosomy X (Zinn et al. 1994). Finally, RPL6 was mapped to a critical region for Noonan syndrome (Jamieson et al. 1994; Kenmochi et al. 2000), and because of similarities between the Noonan and Turner phenotypes (Noonan 1968; Allanson 1987), the gene is considered an attractive candidate for the disease. Although involvement of the RP genes in the pathogenesis of the aforementioned diseases has yet to be proved, we are intrigued by the possibility that defects in other RP genes might also underlie certain pathological conditions. To explore this possibility, we mapped all human RP genes to the chromosomes and then compared the assigned positions with candidate regions for Mendelian disorders (Kenmochi et al. 1998; Uechi et al. 2001). The results emphasize the need to conduct systematic analysis of the genomic sequences of these genes to screen for mutations that could disturb ribosomal function. In the present study, we determined the genomic sequences of human RP genes, as well as the full-length cDNA sequences. Together with the previously determined sequences, we analyzed the characteristics of 73 RP genes with respect to intron/exon structure, transcription start site, promoter region, and the 5′ and 3′ noncoding regions. Comparative analysis of these genes among several eukaryotes was also carried out. Finally, we evaluated the currently available draft genome sequence using our data set of RP gene sequences.