The structure of the gene encoding chicken ribosomal protein L30

Isolation and characterization of chicken GA-binding protein

We have purified and characterized chicken liver nuclear proteins that bind to Ets binding sites (EBSs) of ribosomal protein (r-protein) gene promoters. We employed supershift assays and antibodies to mouse GA binding protein (GABP), to show that the proteins were similar to alpha and beta subunits of GABP. Western blot analysis identified 54- and 38-kDa proteins as the alpha type, and a 46-kDa protein as the beta type. When compared with nuclear extracts (NEs) of other species, we observed that the 38-kDa protein was unique to chicken, and appears to be derived from the 54-kDa protein. The 54- and 46-kDa proteins were highly expressed in chicken tissues and were major components through higher animals, indicating that both proteins have a conserved role.

The human ribosomal protein genes: sequencing and comparative analysis of 73 genes

The ribosome, as a catalyst for protein synthesis, is universal and essential for all organisms. Here we describe the structure of the genes encoding human ribosomal proteins (RPs) and compare this class of genes among several eukaryotes. Using genomic and full-length cDNA sequences, we characterized 73 RP genes and found that (1) transcription starts at a C residue within a characteristic oligopyrimidine tract; (2) the promoter region is GC rich, but often has a TATA box or similar sequence element; (3) the genes are small (4.4 kb), but have as many as 5.6 exons on average; (4) the initiator ATG is in the first or second exon and is within plus minus 5 bp of the first intron boundaries in about half of cases; and (5) 5'- and 3'-UTRs are significantly smaller (42 bp and 56 bp, respectively) than the genome average. Comparison of RP genes from humans, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae revealed the coding sequences to be highly conserved (63% homology on average), although gene size and the number of exons vary. The positions of the introns are also conserved among these species as follows: 44% of human introns are present at the same position in either D. melanogaster or C. elegans, suggesting RP genes are highly suitable for studying the evolution of introns.

Isolation and characterization of medaka ribosomal protein S3a (fte-1) cDNA and gene

Many ribosomal protein genes were cloned from different organisms. We describe here, for the first time, the isolation of the ribosomal protein S3a cDNA and gene from a teleost - the medaka (Oryzias latipes). The cDNA sequence is 863bp long and encodes an open reading frame of 266 amino acids. The gene is 2927bp long and contains six introns and five introns. The levels of the S3a mRNA are elevated during embryonal development. Transcription of the gene was also detected in different tissues of adult medaka. At the 5' untranslated region of the cDNA, the terminal pyrimidine tract, a common feature with all ribosomal protein genes, was found. snoRNA sequences were found in introns 3 and 5, similar to human and mouse U73b and U73a.

Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome

We have determined the organization and sequence of the region containing two ribosomal protein (rp) genes in the human and mouse genomes. The two genes, human RPL13A and RPS11, and mouse Rpl13a and Rps11, are tandemly located in both genomes with an interval of only 4.6kb in the case of the human genes and 1.6kb in the case of the mouse genes. The human RPL13A and RPS11 are 4236bp and 3254bp in length and comprise eight and five exons respectively, whereas the mouse Rps11 is 1951bp long and has five exons. Structural comparison of these genes, including previously reported mouse Rpl13a, revealed a significant conservation of sequences in the promoter regions. Although most rp genes are dispersed throughout the human genome, the conserved features and adjacent localization indicate possible coordinate transcription of the two genes. Furthermore, we have found that four small nucleolar RNA (snoRNA) genes are located in the introns of the two rp genes, both human and mouse. U32, U33, and U34 snoRNAs are encoded in introns 2, 4, and 5 of RPL13A respectively, and U35 in the sixth intron of RPL13A and the third intron of RPS11. The same organization of these snoRNA genes was also observed in the case of the mouse genes.

The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation

Eukaryotic cells contain a large number of small nucleolar RNAs (snoRNAs). A major family of snoRNAs features a consensus ACA motif positioned 3 nucleotides from the 3' end of the RNA. In this study we have characterized nine novel human ACA snoRNAs (U64-U72). Structural probing of U64 RNA followed by systematic computer modeling of all known box ACA snoRNAs revealed that this class of snoRNAs is defined by a phylogenetically conserved secondary structure. The ACA snoRNAs fold into two hairpin structures connected by a single-stranded hinge region and followed by a short 3' tail. The hinge region carries an evolutionarily conserved sequence motif, called box H (consensus, AnAnnA). The H box, probably in concert with the flanking helix structures and the ACA box characterized previously, plays an essential role in the accumulation of human U64 intronic snoRNA. The correct processing of a yeast ACA snoRNA, snR36, in mammalian cells demonstrated that the cis- and trans-acting elements required for processing and accumulation of ACA snoRNAs are evolutionarily conserved. The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., GAR1) suggests that these RNAs possess closely related nucleolar functions.

A characterization of transcriptional regulatory elements in chicken ribosomal protein L37a gene

Transcriptional control elements of chicken ribosomal protein L37a gene were characterized in terms of their activities to promote transcription and their protein binding activities. The region -120 to +168 was necessary for the maximal expression of the promoter-less CAT gene in a transfected chicken cell line. Using the DNase I protection assay, we identified nine protein binding regions distributed in a wide range of -122 to +195. The sequences of most of the elements are conserved among many vertebrate ribosomal protein genes at similar positions of the promoters. These common control elements and their binding proteins may coordinate the expression of ribosomal protein genes.

Lymphocyte p56L32 is a RNA/DNA-binding protein which interacts with conserved elements of the murine L32 ribosomal protein mRNA

In previous studies of the ribosomal protein L32 mRNA, we demonstrated that a conserved polypyrimidine tract found in the 5'-untranslated region (5'-UTR) was required for translational regulation in vivo and that a 56-kDa protein (p56L32) from T-lymphocytes specifically interacts with this sequence [Kaspar, R. L., Kakegawa, T., Cranston, H., Morris, D. R. & White, M. W. (1992) J. Biol. Chem. 267, 508-514]. Here we show that p56L32 binding to the L32 5'-UTR is complex and requires other 5'-UTR RNA sequences in conjunction with the polypyrimidine tract. Deletion and site-directed mutagenesis studies revealed that binding of p56L32 to the L32 5'-UTR requires a second RNA element, GGUGGCUGCC, 15 nucleotides downstream from the polypyrimidine tract. In contrast, L32 RNA transcripts altered in this downstream element were good substrates for binding of the polypyrimidine binding proteins from HeLa nuclear extracts, indicating that these proteins have RNA-binding specificities distinct from p56L32. Competition analysis demonstrated that p56L32 will bind to DNA as well as RNA with identical sequence specificity and similar affinity. Single or double-stranded DNAs composed of the L32 5'-UTR sequences were found to specifically compete with L32 RNA transcripts for p56L32 binding. The L32 5'-UTR downstream element, GGUGGCUGCC, which is required for p56L32 binding, has previously been implicated as a transcriptional element of the L32 gene. The ability of p56L32 to bind this sequence as DNA or RNA suggests p56L32 may have a dual role in the regulation of ribosomal protein mRNA accumulation and translation.