The DNA sequences of eight yeast ribosomal protein genes have been compared for the purpose of identifying homologous regions which may be involved in the coordinate regulation of ribosomal protein synthesis. A 12 bp homology was identified in the 5' DNA sequence preceding the structural gene for 6 out of 8 yeast ribosomal protein genes. In each case the homologous sequence was found at a position approximately 300 bp preceding the transcription start of the ribosomal protein gene. This homology was not identified in any non-ribosomal protein gene examined. Additional homologies between ribosomal protein genes were identified in the transcribed regions, including the untranslated 5' and 3' DNA regions flanking the coding regions.

Computer analysis has previously revealed the presence of a 12-nucleotide common sequence element (AACATCTGCATGACA; HOMOL1) in the upstream regions of several yeast ribosomal protein genes. By extending the sequence analysis of the 5'-flanking regions of a number of other ribosomal protein genes (including those encoding S10-1, S10-2, S33 and L16-2) we could establish that HOMOL1 occurs upstream of most but not all yeast ribosomal protein genes. Apart from HOMOL1 an additional conserved sequence (ACCCATACATTTA; RPG-box) was detected in front of nearly all yeast ribosomal protein genes, although in some cases it is present in the opposite orientation in the other strand. There seems to be no correlation between the occurrence of one box and that of the other. However when both boxes are present the RPG-box is always located 3' to the HOMOL1-sequence mostly at a distance of only a few nucleotides. A further one-to-one comparison of the upstream regions of several yeast ribosomal protein genes revealed extensive additional sequence homologies that are suggested to be involved in the coordinate control of ribosomal protein gene expression in yeast.

From previous studies on cloned yeast ribosomal protein genes we obtained evidence that a large number of them contain an intron [Bollen et al. (1982) Gene 18, 29-38]. In the temperature-sensitive rna2-mutant transcription of these genes leads to the accumulation of precursor RNAs at the restrictive temperature. These precursor mRNAs are several hundreds of nucleotides longer than the respective mature mRNAs. The split character of one of these ribosomal protein genes, viz. the gene coding for the major phosphorylated small-subunit protein S10, was further established by sequence analysis. The intervening sequence interrupts the coding sequence after the second codon and has a length of 352 nucleotides. Genomic Southern hybridizations with a DNA fragment carrying part of the S10-gene revealed that this gene is duplicated on the yeast genome. The molecular weight of S10 as deduced from the sequence analysis was estimated to be 31462 dal. Comparison of the N-terminal aminoacid sequence of the yeast ribosomal protein S10 with that of ribosomal protein S6 from rat liver revealed a striking homology between both proteins. Moreover, at the C-terminal end of the yeast ribosomal protein the sequence Arg-Ala-Ser-Ser-Leu-Lys is present which is very similar to the phosphorylation site of the rat liver protein S6.

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The primary structure of the genes encoding the yeast ribosomal proteins L17a and L25 was determined, as well as the positions of the 5'- and 3'-termini of the corresponding mRNAs. Comparison of the gene sequences to those obtained for various other yeast ribosomal protein genes revealed several similarities. In all split genes the intron is located near the 5'-side of the amino acid coding region. Among the introns a clear pattern of sequence conservation can be observed. In particular the intron-exon boundaries and a region close to the 3'-splice site show sequence homology. Conserved sequences were also found in the leader and trailer regions of the ribosomal protein mRNAs. The 5'-flanking regions of the yeast ribosomal protein genes appeared to contain sequence elements that many but not all ribosomal protein genes have in common, and therefore may be implicated in the coordinate expression of these genes. The amino acid coding sequences of the ribosomal protein genes show a biased codon usage. Like most yeast ribosomal protein molecules, L17a and L25 are particularly basic at their N-terminus.