Chromosomal distribution of ribosomal protein genes in the mouse

Regulation of ribosomal protein mRNA content and translation in growth-stimulated mouse fibroblasts

When resting (G0) mouse 3T6 fibroblasts are serum stimulated to reenter the cell cycle, the rates of synthesis of rRNA and ribosomal proteins increase, resulting in an increase in ribosome content beginning about 6 h after stimulation. In this study, we monitored the content, metabolism, and translation of ribosomal protein mRNA (rp mRNA) in resting, exponentially growing, and serum-stimulated 3T6 cells. Cloned cDNAs for seven rp mRNAs were used in DNA-excess filter hybridization studies to assay rp mRNA. We found that about 85% of rp mRNA is polyadenylated under all growth conditions. The rate of labeling of rp mRNA relative to total polyadenylated mRNA changed very little after stimulation. The half-life of rp mRNA was about 11 h in resting cells and about 8 h in exponentially growing cells, values which are similar to the half-lives of total mRNA in resting and growing cells (about 9 h). The content of rp mRNA relative to total mRNA was about the same in resting and growing 3T6 cells. Furthermore, the total amount of rp mRNA did not begin to increase until about 6 h after stimulation. Since an increase in rp mRNA content did not appear to be responsible for the increase in ribosomal protein synthesis, we determined the efficiency of translation of rp mRNA under different conditions. We found that about 85% of pulse-labeled rp mRNA was associated with polysomes in exponentially growing cells. In resting cells, however, only about half was associated with polysomes, and about 30% was found in the monosomal fraction. The distribution shifted to that found in growing cells within 3 h after serum stimulation. Similar results were obtained when cells were labeled for 10.5 h. About 70% of total polyadenylated mRNA was in the polysome fraction in all growth states regardless of labeling time, indicating that the shift in mRNA distribution was species specific. These results indicate that the content and metabolism of rp mRNA do not change significantly after growth stimulation. The rate of ribosomal protein synthesis appears to be controlled during the resting-growing transition by an alteration of the efficiency of translation of rp mRNA, possibly at the level of protein synthesis initiation.

Regulation of ribosomal protein mRNA content and translation in growth-stimulated mouse fibroblasts

When resting (G0) mouse 3T6 fibroblasts are serum stimulated to reenter the cell cycle, the rates of synthesis of rRNA and ribosomal proteins increase, resulting in an increase in ribosome content beginning about 6 h after stimulation. In this study, we monitored the content, metabolism, and translation of ribosomal protein mRNA (rp mRNA) in resting, exponentially growing, and serum-stimulated 3T6 cells. Cloned cDNAs for seven rp mRNAs were used in DNA-excess filter hybridization studies to assay rp mRNA. We found that about 85% of rp mRNA is polyadenylated under all growth conditions. The rate of labeling of rp mRNA relative to total polyadenylated mRNA changed very little after stimulation. The half-life of rp mRNA was about 11 h in resting cells and about 8 h in exponentially growing cells, values which are similar to the half-lives of total mRNA in resting and growing cells (about 9 h). The content of rp mRNA relative to total mRNA was about the same in resting and growing 3T6 cells. Furthermore, the total amount of rp mRNA did not begin to increase until about 6 h after stimulation. Since an increase in rp mRNA content did not appear to be responsible for the increase in ribosomal protein synthesis, we determined the efficiency of translation of rp mRNA under different conditions. We found that about 85% of pulse-labeled rp mRNA was associated with polysomes in exponentially growing cells. In resting cells, however, only about half was associated with polysomes, and about 30% was found in the monosomal fraction. The distribution shifted to that found in growing cells within 3 h after serum stimulation. Similar results were obtained when cells were labeled for 10.5 h. About 70% of total polyadenylated mRNA was in the polysome fraction in all growth states regardless of labeling time, indicating that the shift in mRNA distribution was species specific. These results indicate that the content and metabolism of rp mRNA do not change significantly after growth stimulation. The rate of ribosomal protein synthesis appears to be controlled during the resting-growing transition by an alteration of the efficiency of translation of rp mRNA, possibly at the level of protein synthesis initiation.

Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes

We have identified a new class of ribosomal protein (RP) genes that appear to have been retrotransposed from X-linked RP genes. Mammalian ribosomes are composed of four RNA species and 79 different proteins. Unlike RNA constituents, each protein is typically encoded by a single intron- containing gene. Here we describe functional autosomal copies of the X-linked human RP genes, which we designated RPL10L (ribosomal protein L10-like gene), RPL36AL and RPL39L after their progenitors. Because these genes lack introns in their coding regions, they were likely retrotransposed from X-linked genes. The identities between the retrotransposed genes and the original X-linked genes are 89-95% in their nucleotide sequences and 92-99% in their amino acid sequences, respectively. Northern blot and PCR analyses revealed that RPL10L and RPL39L are expressed only in testis, whereas RPL36AL is ubiquitously expressed. Although the role of the autosomal RP genes remains unclear, they may have evolved to compensate for the reduced dosage of X-linked RP genes.

Analysis of 148 kb of Genomic DNA Around the wnt1 Locus of Fugu rubripes

The analysis of the sequence of ∼150 kb of a genomic region corresponding to the wnt1 gene of the Japanese pufferfishFugu rubripes confirms the compact structure of the genome. Fifteen genes were found in this region, and 26.6% of the analyzed sequence is coding sequence. With an average intergenic distance of <5 kb, this gene density is comparable to that ofCaenorhabditis elegans. The compactness of this region corresponds to the reduction of the overall size of the genome, consistent with the conclusion that the gene number in Fuguand human genomes is approximately the same. Eight of the genes have been mapped in the human genome and all of them are found in the chromosomal band 12q13, indicating a high degree of synteny in both species, Fugu and human. Comparative sequence analysis allows us to identify potential regulatory elements for wnt1 andARF3, which are common to fish and mammals.

[The sequence data described in this paper have been submitted to GenBank under accession no. AF056116.]

The intron-containing ribosomal protein-encoding genes L5, L7a and L37a are unlinked in chicken

Chicken ribosomal protein (rp)-encoding genes are currently being studied at the nucleotide level and three independent recombinant phages have been isolated from chicken genomic libraries using cloned cDNA probes. Each of these was shown to include an intron-containing rp gene of chicken (L5, L7a, L37a). In this study the chromosomal location of these three intron-containing rp from the large subunit of the chicken ribosome was determined by fluorescence in situ hybridization. L7a mapped to a microchromosome, whereas L5 and L37a mapped to macrochromosomes 8 and 7, respectively. The results demonstrate that these functionally related genes are widely dispersed in the genome. Furthermore, as in the case of many other evolutionarily advanced eukaryotes, there is no apparent linkage of rp and rRNA genes.

Mapping of ribosomal protein S3 and internally nested snoRNA U15A gene to human chromosome 11q13.3-q13.5

The mammalian ribosome is a massive structure composed of 4 RNA species and about 80 different proteins. One of these ribosomal proteins, S3, appears to function not only in translation but also as an endonuclease in repair of UV-induced DNA damage. Moreover, the first intron of human RPS3 transcripts is processed to generate U15A, a small nucleolar RNA. We localized the nested RPS3/U15A genes to the immediate vicinity of D11S356 and D11S533 on human chromosome 11q13.3-q13.5 using a combination of somatic cell hybrid analysis, fluorescence in situ hybridization, and YAC/STS content mapping. These findings add to the evidence that genes encoding ribosomal proteins are scattered about the human genome.

Identification and genetic mapping of 151 dispersed members of 16 ribosomal protein multigene families in the mouse

More than 150 individual members of 16 ribosomal protein multigene families were identified as DNA restriction fragments and genetically mapped. The ribosomal protein gene-related sequences are widely dispersed throughout the mouse genome. Map positions were determined by analysis of 144 progeny mice from both an interspecific (C57BL/6J x SPRET/Ei)F1 x SPRET/Ei and an intersubspecific (C57BL/6J x CAST/Ei)F1 x C57BL/6J backcross. In addition, 30 members of the multigene families encoding PGK1 ODC, and TPI, including five new loci for ODC and one new locus for TPI, were characterized and mapped. Interspecific backcross linkage data for 29 nonecotropic murine leukemia retroviruses endogenous to C57BL/6J mice are also reported. Transmission ratio distortions and recombination frequencies are compared between the two backcrosses.

Sequence analysis of mouse cDNAs encoding ribosomal proteins L12 and L18

Mouse cDNAs encoding ribosomal proteins (r-proteins), L12 and L18, were isolated and their sequences determined. The L12 cDNA was found to contain 639 bp, including a coding sequence of 498 nucleotides (nt), 5' (78 nt) and 3' (45 nt) untranslated regions (UTRs), and a poly(A) tail of 18 nt. The L18 cDNA was shown to consist of 648 bp, including a coding sequence of 567 nt, 5' (26 nt) and 3' (39 nt) UTRs, and a poly(A) tail of 16 nt. The nt sequences of the protein-coding region from the mouse L12 and L18 cDNAs were found to exhibit 96% and 92% identity, respectively, with those of the rat. With the use of mouse L12 and L18 cDNA probes, multiple (at least 10) copies of the L12 and L18 gene families were shown to be present in the mouse and rat genomes. However, there was no sequence heterogeneity detected among seven L18 cDNA clones, indicating that only one copy of the L18 gene-related sequences is functional, and the other copies are presumably nonfunctional pseudogenes. The complete amino acid (aa) sequences of the mouse r-proteins, L12 and L18, were deduced from the nt sequences of their cDNA clones. L12 has 165 aa and a M(r) of 17,790, while L18 has 188 aa and a M(r) of 21,570. The aa sequences of the mouse r-proteins, L12 and L18, exhibit 98% and 94% identity, respectively, to those of rat.

The mapping of seven intron-containing ribosomal protein genes shows they are unlinked in the human genome

Mammalian ribosomal protein (rp) genes are members of multigene families which are composed predominantly of multiple processed pseudogenes and one functional intron-containing gene. The presence of multiple pseudogenes has hampered the isolation and study of the functional rp genes. We have recently developed a polymerase chain reaction (PCR)-based strategy for the detection of intron-containing genes in the presence of multiple pseudogenes (B. Davies, S. Feo, E. Heard, and M. Fried, 1989, Proc. Natl. Acad. Sci. USA 86: 6691-6695). We have used this technique to identify the intron-containing PCR products of seven human rp genes (rpL19, rpL30, rpL35a, rpL36a, rpS6, rpS11, rpS17) and to map their chromosomal locations. No linkage was found between any of these seven rp genes nor was linkage found to the three other rp genes previously mapped. The wide distribution of the rp genes throughout the human genome strongly suggests that the coordinate regulation of the expression of mammalian ribosomal proteins in response to the cell's varying requirements for protein synthesis is not a result of cis activation of chromosomal regions but is mediated by trans-acting factors.

Expression of ribosomal protein genes in mouse oocytes and early embryos

The quantitative changes in the mRNAs for ribosomal proteins L7a, L18a, and S15 were assayed in slot hybridization experiments using labeled cRNA probes with total RNA from late growth-phase oocytes, ovulated eggs, and early embryos through the blastocyst stage. All three mRNAs showed a similar developmental pattern of prevalence, but their copy numbers per oocyte or embryo fluctuated according to developmental stage. There are on an average about 17,000 copies of each mRNA in the late growth-phase oocyte; this number drops to one-fifth to one-tenth in the ovulated egg and two-cell embryo but increases rapidly during cleavage to bout 25,000 in the eight-cell embryo and about 42,000 in the blastocyst. A comparison of the levels of these mRNAs with the reported rates of ribosomal protein synthesis (LaMarca and Wassarman, 1979) suggests that, in late growth-phase oocytes, ribosomal protein synthesis is regulated primarily at the translational level and is kept low by some factor limiting mRNA utilization. On the other hand, the high rate of ribosome biosynthesis during early embryogenesis from the two-cell stage onward appears to involve the coordinate activation and transcription of ribosomal RNA and ribosomal protein genes coupled with the immediate translational utilization of ribosomal protein mRNAs.

The murine MHC encodes a mammalian homolog of bacterial ribosomal protein S13

The mouse major histocompatibility complex (MHC) contains many genes in addition to the classical immune response genes. We have screened overlapping cosmid clones covering 170 kb of the H-2K region for genes expressed in embryonal carcinoma (EC) cells. The Ke-3 gene (Abe et al. 1988) found in this region was further studied by Southern, Northern, and sequence analysis. It is an expressed, intron-containing locus encoding a mouse homolog of the bacterial ribosomal protein S13. This is the first non-organelle S13 homolog identified in metazoans, and its genomic location has been determined precisely.

Homologous ribosomal protein genes on the human X and Y chromosomes: escape from X inactivation and possible implications for Turner syndrome

We have isolated two genes on the human sex chromosomes, one on the Y and one on the X, that appear to encode isoforms of ribosomal protein S4. These predicted RPS4Y and RPS4X proteins differ at 19 of 263 amino acids. Both genes are widely transcribed in human tissues, suggesting that the ribosomes of human males and females are structurally distinct. Transcription analysis revealed that, unlike most genes on the X chromosome, RPS4X is not dosage compensated. RPS4X maps to the long arm of the X chromosome (Xq), where no other genes are known to escape X inactivation. Curiously, RPS4X maps near the site from which the X-inactivating signal is thought to emanate. On the Y chromosome, RPS4Y maps to a 90 kb segment that has been implicated in Turner syndrome. We consider the possible role of RPS4 haploinsufficiency in the etiology of the Turner phenotype.

A ribosomal protein gene family from Schizosaccharomyces pombe consisting of three active members

Recently, we have reported the isolation and characterization of a ribosomal protein gene from the fission yeast Schizosaccharomyces pombe. This gene was called K37. Here we describe the isolation of two genes which are related to the K37 gene. Sequence analysis of these genes revealed open reading frames encoding proteins which are almost identical to the ribosomal protein K37. Furthermore, all three genes are functional as determined by Northern analysis using transformed and wild type cells. The results indicate that S. pombe contains a ribosomal protein gene family, designated the K-family, consisting of three active members. The promoter regions of the three members are compared and several common motifes are identified which might serve as transcriptional activators in these genes.

The transcriptionally active human ribosomal protein S17 gene

A human ribosomal protein S17 cDNA [Chen et al., Proc. Natl. Acad. Sci. USA 83 (1986) 6907-6911] was used to isolate four S17 DNA clones from human genomic libraries constructed in bacteriophage lambda and cosmid vectors. Based on its transcriptional activity in a transient expression assay and on sequence similarity with S17 cDNA, cosmid clone HGS17-6 was identified as carrying the functional RPS17 gene. RPS17 is composed of five exons and four introns that span 4 kb of DNA. Two lambda clones of human genomic DNA were recognized as containing processed S17 pseudogenes, because (i) they were transcriptionally inactive in the transient assay, and (ii) they possess multiple, perfectly spliced RPS17 exons. Their coding sequences differ slightly from the cDNA and functional genomic clone.

Isolation and structural analysis of a ribosomal protein gene in D.melanogaster

By using the cDNA clone containing the sequence for the L1 ribosomal protein gene of Xenopus laevis as probe (1), we have isolated positive phages from a Drosophila melanogaster genomic library. The Drosophila genomic fragment, which gives the hybridization signal with the Xenopus cDNA, was sequenced: a region of 369 bp is 70% homologous to the sequence of X. laevis L1 cDNA. The gene was localized in situ at position 98AB of the right arm of the third polytene chromosome. By S1 mapping and heteroduplex analysis we have found that the gene is interrupted by three introns. A Drosophila cDNA embryonic library was screened and three cDNA clones were isolated (900, 1400 and 1500 nt long). By Northern analysis the cDNAs identify a 1400nt transcript present at every stage of development. By the features described, the clones we have isolated identify the Drosophila rp gene homologous to the L1 rp gene of Xenopus and could code for the L1 ribosomal protein described in D. melanogaster.

Rat ribosomal protein L35a multigene family: molecular structure and characterization of three L35a-related pseudogenes

The rat ribosomal protein L35a gene comprises a multigene family which contains 15-20 members as shown by the Southern blot analysis using L35a cDNA as a probe. We isolated 15 independent clones which contained distinct genes from a rat genomic library. Analysis of the restriction sites showed that all of them lacked the intervening sequences. Thermal stability of the hybrid molecules between these genes and the cDNA indicated that the similarity of the genes to the cDNA sequence varied. The nucleotide sequences of three genes gRL35a-A, gRL35a-B and gRL35a-G were determined. They shared some characteristics; namely: they lacked the intervening sequences, they contained (A)-rich tracts, and they were flanked by direct repeats. Two genes, gRL35a-A and gRL35a-B, contained a sequence completely identical to that of the cDNA. The nucleotide sequence of the 5' flanking region of gRL35a-B showed a significant homology with that of the same region of mouse ribosomal protein L32-related unmutated processed genes. Although this region of gRL35a-B contained the sequences homologous to the TATA box and the CCAAT box, gRL35a-B was not transcribed in an in vitro assay system. Thus, the L35a gene family comprises mostly processed pseudogenes. Further, Southern blot analysis in various animals indicated that the multigene construction of this ribosomal protein gene was a feature of mammalian genes. The origin and the evolutionary aspect of processed pseudogenes are discussed.

Three functional ribosomal protein genes are unlinked in mouse genome

The mouse chromosomes bearing three functional ribosomal protein (rp) genes were identified by Southern blot analysis of DNA from a panel of mouse-hamster hybrid cell lines. Unique sequence intron probes were used to distinguish the functional rp genes from their multiple processed pseudogene counterparts. The genes specifying ribosomal proteins S16, L30, and L32 were found to be on chromosomes 7, 15, and 6, respectively. Since these functional rp genes are widely dispersed in the mouse genome, coordinate regulation of their transcriptional activity cannot be accomplished by a structural alteration of a single chromosomal region. Rather, it would have to involve interactions with sequences or structural motifs that are common to all three genes.

Characterization of the multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene counterparts by an analysis of total genomic DNA

Two genes from the family encoding mouse ribosomal protein S16 were cloned, sequenced, and analyzed. One gene was found to be a processed pseudogene, i.e., a nonfunctional gene presumably derived from an mRNA intermediate. The other S16 gene contained introns and had exonic sequences identical to those of a cloned S16 cDNA. The expression of this gene was demonstrated by Northern blot analysis of nuclear poly(A)+ RNA with cDNA and unique sequence intron probes. Each S16 intron contains a well-preserved remnant of the TACTAAC motif, which is ubiquitous in yeast introns and known to play a critical role in intron splicing. A sequence comparison with two other mouse ribosomal protein genes analyzed in our laboratory, L30 and L32, revealed common structural features which might be involved in the control and coordination of ribosomal protein gene expression. These include the lack of a canonical TATA box in the -20 to -30 region and a remarkably similar 12-nucleotide pyrimidine sequence (CTTCCYTYYTC) that spans the cap site and is flanked by C + G-rich sequences. The nature of the other members of the S16 family was evaluated by three types of experiment: a DNase I sensitivity analysis to measure the extent of chromatin condensation; an analysis of the thermal stability of cDNA-gene hybrids to estimate the extent of divergence of each gene sequence from that of the expressed gene; and a restriction fragment analysis which distinguishes intron-containing genes from intronless processed genes. The results of these analyses show that all genes except the expressed S16 gene are in a condensed chromatin configuration associated with transcriptional quiescence; that most of the genes within the S16 family have sequences greater than 7% divergent from the expressed S16 gene; and that at least 7 of the 10 S16 genes lack introns. We conclude that the ribosomal protein S16 multigene family contains one expressed intron-containing gene and nine inactive pseudogenes, most or all of which are of the processed type.

Posttranscriptional regulation and assembly into ribosomes of a Saccharomyces cerevisiae ribosomal protein-beta-galactosidase fusion

To study the regulation of ribosomal protein genes, we constructed a 'lacZ fusion of the Saccharomyces cerevisiae RP51A gene, containing the first 64 codons of RP51A. In a strain lacking an intact RP51A gene (cells are viable due to the presence of an active RP51B gene), beta-galactosidase activity is 10-fold greater than in a strain containing RP51A. RP51A-lacZ mRNA levels are equal in the two strains, indicating that regulation is posttranscriptional. In the absence of the RP51A gene, the fusion protein is predominantly cytoplasmic and associated with polysomes, whereas in the presence of RP51A, the fusion protein is predominantly nuclear, and none is associated with polysomes. Deletions were made in the RP51A-coding portion of the fusion gene. The most extensively deleted gene, containing only the first seven RP51A codons fused to lacZ, produced a high level of beta-galactosidase activity in both the presence and the absence of the RP51A gene. In both cases, little or none of this shorter fusion protein was found associated with polysomes. Thus, a regulatory site (or sites) lies in the protein-coding region of RP51A. We suggest that posttranscriptional regulation of the rp51 fusion protein is related to assembly of the protein into ribosomes.

Ribosomal protein gene sequences map to human chromosomes 5, 8, and 17

DNA sequences complementary to six mammalian ribosomal protein (r-protein) cDNAs are assigned to human chromosomal linkage groups in human-Chinese hamster hybrid cell clones. Ten r-protein DNA fragments map to chromosomes 5, 8 and 17, indicating that these important, housekeeping genes are distributed to multiple sites in the human genome. Each of the chromosome assignments, determined initially by surveying Chinese hamster-human hybrid cell clones with complex karyotypes using Chinese hamster and human cDNA probes, were confirmed in critical minipanels of highly reduced or monochromosomal hybrid cells. As all 10 fragments mapped to only three human chromosomes, r-protein sequences appear to be distributed nonrandomly within human DNA. The r-protein S14 sequence assigned to human chromosome 5 (5q23-5q33) rescues Chinese hamster emetine-resistance mutations (emt b) in interspecific hybrids. Therefore, this sequence corresponds to the transcriptionally active human RPS14 gene. In contrast, other r-protein DNA sequences examined likely are a mixture of functional genes and inactive pseudogenes.

Characterisation of an mRNA encoding a human ribosomal protein homologous to the yeast L44 ribosomal protein

We describe the isolation and characterisation of a full-length cDNA sequence (pZH-21) of a human ribosomal protein (rp) mRNA isolated from a cDNA library constructed from the human ZR-75-1 mammary tumour cell-line. The predicted protein is highly basic and shows 72% homology at the amino acid (aa) level with yeast rp L44. Comparative RNA blotting of ZR-75-1 poly(A)+ RNA isolated from cells cultured in the presence of the anti-oestrogen tamoxifen demonstrates the presence of a number of mRNA species whose concentration is elevated co-ordinately 5-6-fold in the presence of 17beta-oestradiol. Insulin in the presence of tamoxifen, also enhanced rp mRNA levels suggesting increased levels are a reflection of cell proliferation as opposed to specific hormonal regulation. Genomic analysis demonstrates the presence of a family of related human sequences, and homology with rat and guinea pig rp genes, but not yeast DNA. The conservation of rp aa sequence, in the absence of detectable homology at the nucleotide (nt) level, points to an important common functional role of the L44 protein in ribosome structure and function in man and yeast.

Characterization of the multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene counterparts by an analysis of total genomic DNA

Two genes from the family encoding mouse ribosomal protein S16 were cloned, sequenced, and analyzed. One gene was found to be a processed pseudogene, i.e., a nonfunctional gene presumably derived from an mRNA intermediate. The other S16 gene contained introns and had exonic sequences identical to those of a cloned S16 cDNA. The expression of this gene was demonstrated by Northern blot analysis of nuclear poly(A)+ RNA with cDNA and unique sequence intron probes. Each S16 intron contains a well-preserved remnant of the TACTAAC motif, which is ubiquitous in yeast introns and known to play a critical role in intron splicing. A sequence comparison with two other mouse ribosomal protein genes analyzed in our laboratory, L30 and L32, revealed common structural features which might be involved in the control and coordination of ribosomal protein gene expression. These include the lack of a canonical TATA box in the -20 to -30 region and a remarkably similar 12-nucleotide pyrimidine sequence (CTTCCYTYYTC) that spans the cap site and is flanked by C + G-rich sequences. The nature of the other members of the S16 family was evaluated by three types of experiment: a DNase I sensitivity analysis to measure the extent of chromatin condensation; an analysis of the thermal stability of cDNA-gene hybrids to estimate the extent of divergence of each gene sequence from that of the expressed gene; and a restriction fragment analysis which distinguishes intron-containing genes from intronless processed genes. The results of these analyses show that all genes except the expressed S16 gene are in a condensed chromatin configuration associated with transcriptional quiescence; that most of the genes within the S16 family have sequences greater than 7% divergent from the expressed S16 gene; and that at least 7 of the 10 S16 genes lack introns. We conclude that the ribosomal protein S16 multigene family contains one expressed intron-containing gene and nine inactive pseudogenes, most or all of which are of the processed type.

Posttranscriptional regulation and assembly into ribosomes of a Saccharomyces cerevisiae ribosomal protein-beta-galactosidase fusion

To study the regulation of ribosomal protein genes, we constructed a 'lacZ fusion of the Saccharomyces cerevisiae RP51A gene, containing the first 64 codons of RP51A. In a strain lacking an intact RP51A gene (cells are viable due to the presence of an active RP51B gene), beta-galactosidase activity is 10-fold greater than in a strain containing RP51A. RP51A-lacZ mRNA levels are equal in the two strains, indicating that regulation is posttranscriptional. In the absence of the RP51A gene, the fusion protein is predominantly cytoplasmic and associated with polysomes, whereas in the presence of RP51A, the fusion protein is predominantly nuclear, and none is associated with polysomes. Deletions were made in the RP51A-coding portion of the fusion gene. The most extensively deleted gene, containing only the first seven RP51A codons fused to lacZ, produced a high level of beta-galactosidase activity in both the presence and the absence of the RP51A gene. In both cases, little or none of this shorter fusion protein was found associated with polysomes. Thus, a regulatory site (or sites) lies in the protein-coding region of RP51A. We suggest that posttranscriptional regulation of the rp51 fusion protein is related to assembly of the protein into ribosomes.

P31, a mammalian housekeeping protein encoded by a multigene family containing a high proportion of pseudogenes

The primary structure of P31, a 13.300 kDa mammalian 'housekeeping' protein, was deduced from the nucleotide sequence of a rat recombinant cDNA clone. The P31 mRNA has 950 nucleotides and codes for a protein of 121 amino acids. This mRNA is present in several mouse tissues and in other mammals. Nuclei of rapidly growing cells contain mature P31 mRNA and a distinctive set of larger transcripts. P31 is encoded by a multigene family. Five members of the family were isolated from a mouse genomic library and restriction mapping and S1 nuclease analysis of four of them (P31-4, P31-12, P31-13 and P31-14) suggest that they are processed genes. The very low homology of the fifth (P31-8) with respect to the corresponding cDNA sequence indicates that it is a pseudogene. Although the features of the mRNA and the genes encoding P31 exhibit extensive similarity with those of ribosomal proteins, neither the identity nor the biological function of the protein has yet been determined.

Synthesis and incorporation of human ribosomal protein S14 into functional ribosomes in human-Chinese hamster cell hybrids containing human chromosome 5: human RPS14 gene is the structural gene for ribosomal protein S14

In Chinese hamster ovary cells, mutations in the RPS14 gene (which was previously designated emtB) render cells resistant to normally cytotoxic concentrations of the protein synthesis inhibitor, emetine. Several lines of evidence indicate the RPS14 gene in Chinese hamster is the structural gene for ribosomal protein S14, including the finding that mutants with alterations in this gene produce an electrophoretically altered form of this protein. A human gene which complements the defect in CHO RPS14 mutants and renders them sensitive to emetine has previously been assigned to the long arm of chromosome 5. The analysis of ribosomal proteins extracted from CHO Emtr X human cell hybrids, which contain human chromosome 5 and are emetine sensitive, demonstrated the presence of both the normal human and altered hamster forms of ribosomal protein S14. Human chromosome 5, the emetine-sensitive phenotype, and the human form of ribosomal protein S14 segregate concordantly from hybrids, confirming that the human gene in question is the structural gene for this protein. In addition, the results indicate that in interspecific cell hybrids, the human form of S14 is either incorporated into functional ribosomes more efficiently than the altered hamster protein or the human gene is overexpressed relative to the corresponding hamster gene.

Cloning of cDNA encoding a 100 kDa nucleolar protein (nucleoline) of Chinese hamster ovary cells

Nucleoline (100 kDa) is the major nucleolar protein in exponentially growing cells that behaves like a nucleolar organizer protein and plays a key role in rDNA transcription and prerRNA processing. We reported the isolation of 5 cDNA clones by probing a cDNA library, constructed in the expression vector lambda gt11, with a polyclonal serum raised against nucleoline. A new immunoassay, using hybrid proteins (beta gal-cDNA encoded protein) was developed to establish that the isolated cDNAs encoded parts of nucleoline. A further confirmation resulted from the sequence comparison between the cDNA encoded peptide and a 42 aa peptide isolated from rat nucleoline (1). The 5 cDNAs overlapped extensively and covered more than 90% of a full length cDNA. By probing a Northern blot with the 100 kDa cDNA, a 2650 nucleotide polyA+ RNA was detected that contained just enough information to code for nucleoline.

Evolutionary conservation of ribosomal protein mRNA sequences: application for expansion of corresponding cDNA and gene libraries

Cloned cDNAs, containing ribosomal protein sequences from mouse (five cDNAs) or Xenopus laevis (six cDNAs), were used to estimate the evolutionary conservation, from insects to mammals, of the corresponding mRNA sequences. Northern blot analysis reveals a variable degree of homology between these sequences in different eukaryotes. Thus, among the ribosomal protein cDNA clones utilized, some exhibit complete, others partial, and a few no interphyla cross-hybridization. Melting profile analysis was employed to quantitate this homology. It is proposed that for expansion of eukaryotic ribosomal cDNA and gene libraries, one can exploit the interspecies homology of the corresponding sequences. However, the diverse evolutionary conservation of individual ribosomal protein gene sequences should be taken into account.

Isolation and characterization of cloned DNA sequences containing ribosomal protein genes of Drosophila melanogaster

Ribosomal (r) proteins encoded by polyadenylated RNA were specifically precipitated in vitro from polysomes by using antibodies raised against characterized Drosophila melanogaster r proteins. The immuno-purified mRNA in the polysome complex was used to prepare cDNA with which to probe a D. melanogaster genomic library. Selected recombinant phages were used to hybrid select mRNAs, which were analyzed by in vitro translation. Three clones containing the genes for r proteins 7/8, S18, and L12 were positively identified by electrophoresis of the translation products in one-dimensional and two-dimensional polyacrylamide gels. Sequences encoding r proteins S18 and L12 were found to be present in the genome in single copies. In contrast, the polynucleotide containing the region encoding 7/8 may be repeated or may contain or be flanked by short repeated sequences. The sizes of mRNAs that hybridized to the recombinant clone containing 7/8 were significantly larger than would be expected from the molecular weight of protein 7/8, implying that there were unusually long 5' and 3' noncoding sequences. The mRNAs for r proteins S18 and L12 were however, only about 10% larger. In situ hybridizations to salivary gland polytene chromosomes, using the recombinant phage, revealed that the recombinant clone containing the gene for r protein 7/8 hybridized to 5D on the X chromosome; the recombinant clone containing the gene for S18 hybridized to 15B on the same chromosome, and the recombinant phage containing the gene for L12 hybridized to 62E on chromosome 3L. It is of interest that the genomic locations of all three r protein clones were within the chromosomal intervals known to contain the Minute mutations [M(1)0, M(1)30, and M(3)LS2]. Although each clone contained sequences specifying two to four proteins, none had more than one identifiable r protein gene, suggesting that different D. melanogaster r protein genes may not be closely linked.

Characterization of the expressed gene and several processed pseudogenes for the mouse ribosomal protein L30 gene family

Five cloned genes encoding the mouse ribosomal protein L30 were isolated from a recombinant DNA library and characterized by restriction mapping and nucleotide sequence analysis. Only one of these genes has introns and is expressed; the others are inactive processed pseudogenes. The expressed gene consists of five exons and four introns spanning 2,723 nucleotides. Transcripts of this gene are processed into the mature L30 mRNA by pathways that exhibit both constraints and flexibility with regard to the order of intron excision. The L30 mRNA which is 457 to 468 nucleotides in length excluding the polyadenylic acid tail, exhibits some microheterogeneity at its 3' end and encodes a basic protein of 115 amino acids. The 5' portion of the rpL30 gene has some novel features which are remarkably similar to the previously characterized mouse rpL32 gene. These include homologous sequences in the -60 to -340 region, the absence of a good TATA consensus sequence, and the presence of a palindromic pyrimidine sequence that spans the cap site.

Isolation of a mouse DNA fragment with homology to a Drosophila ribosomal protein gene

A mouse genomic library in lambda Charon 4A was screened for putative ribosomal protein genes using a fragment of the gene encoding Drosophila ribosomal protein 49 as a hybridization probe under nonstringent hybridization conditions. A recombinant phage was selected and its restriction enzyme map determined. The major species of mouse poly(A)+ mRNA homologous to the putative gene is about 740 nucleotides long.

Isolation and characterization of cloned DNA sequences containing ribosomal protein genes of Drosophila melanogaster

Ribosomal (r) proteins encoded by polyadenylated RNA were specifically precipitated in vitro from polysomes by using antibodies raised against characterized Drosophila melanogaster r proteins. The immuno-purified mRNA in the polysome complex was used to prepare cDNA with which to probe a D. melanogaster genomic library. Selected recombinant phages were used to hybrid select mRNAs, which were analyzed by in vitro translation. Three clones containing the genes for r proteins 7/8, S18, and L12 were positively identified by electrophoresis of the translation products in one-dimensional and two-dimensional polyacrylamide gels. Sequences encoding r proteins S18 and L12 were found to be present in the genome in single copies. In contrast, the polynucleotide containing the region encoding 7/8 may be repeated or may contain or be flanked by short repeated sequences. The sizes of mRNAs that hybridized to the recombinant clone containing 7/8 were significantly larger than would be expected from the molecular weight of protein 7/8, implying that there were unusually long 5' and 3' noncoding sequences. The mRNAs for r proteins S18 and L12 were however, only about 10% larger. In situ hybridizations to salivary gland polytene chromosomes, using the recombinant phage, revealed that the recombinant clone containing the gene for r protein 7/8 hybridized to 5D on the X chromosome; the recombinant clone containing the gene for S18 hybridized to 15B on the same chromosome, and the recombinant phage containing the gene for L12 hybridized to 62E on chromosome 3L. It is of interest that the genomic locations of all three r protein clones were within the chromosomal intervals known to contain the Minute mutations [M(1)0, M(1)30, and M(3)LS2]. Although each clone contained sequences specifying two to four proteins, none had more than one identifiable r protein gene, suggesting that different D. melanogaster r protein genes may not be closely linked.

Characterization of the expressed gene and several processed pseudogenes for the mouse ribosomal protein L30 gene family

Five cloned genes encoding the mouse ribosomal protein L30 were isolated from a recombinant DNA library and characterized by restriction mapping and nucleotide sequence analysis. Only one of these genes has introns and is expressed; the others are inactive processed pseudogenes. The expressed gene consists of five exons and four introns spanning 2,723 nucleotides. Transcripts of this gene are processed into the mature L30 mRNA by pathways that exhibit both constraints and flexibility with regard to the order of intron excision. The L30 mRNA which is 457 to 468 nucleotides in length excluding the polyadenylic acid tail, exhibits some microheterogeneity at its 3' end and encodes a basic protein of 115 amino acids. The 5' portion of the rpL30 gene has some novel features which are remarkably similar to the previously characterized mouse rpL32 gene. These include homologous sequences in the -60 to -340 region, the absence of a good TATA consensus sequence, and the presence of a palindromic pyrimidine sequence that spans the cap site.

Sequence, structure, and codon preference of the Drosophila ribosomal protein 49 gene

In this communication, we describe several features of the D. melanogaster gene which codes for ribosomal protein 49 (rp49). Nucleotide sequence analysis in conjunction with primer extension and S1 nuclease protection experiments show that the structure of the rp49 gene consists of a 102 bp 5' exon, a single 59 bp intron, and a 420 bp 3' exon, encoding a total of 132 amino acids. The rp49 gene shares many features with other abundantly expressed Drosophila genes, including codon preference, which are discussed.

Isolation and characterization of four mouse ribosomal-protein-L18 genes that appear to be processed pseudogenes

We describe the isolation and initial characterization of six independent lambda Charon 4A recombinant phages which carry four mouse genes for ribosomal protein L18 (L18-15, L18-17, L18-18, L18-30). Structural analysis indicates that these L18 genes contain the entire coding sequence (approx. 600 bp), but lack introns and differ both in their flanking and coding sequences. Based on these features we propose that these are processed pseudogenes. However, we have no indications whether these genes are expressed at either the transcriptional or translational levels. Quantitative estimation of sequence divergence of these genes suggest that the order of their evolutionary emergence (integration) is: first L18-17 and L18-18, then L18-15 and finally L18-30. We discuss the implication of the high proportion of L18 processed genes in this multigene family with respect to the coordinate regulation of r-proteins.

A multigene family of intron lacking and containing genes, encoding for mouse ribosomal protein L7

Mouse ribosomal protein L7 is encoded by a multigene family. Screening of two mouse genomic libraries with cloned L7 cDNA, has resulted in the isolation of nine independent lambda Charon 4A recombinant phages which include seven different L7 genes. Restriction enzyme mapping of six of these genes (L7-1, L7-16, L7-18, L7-28, L7-35 and L7- 16b ) reveals dissimilarity in sites within the L7 sequences as well as in the flanking regions. Electron microscopic analysis of heteroduplex and S1 nuclease mapping demonstrate that the first five genes contain the entire L7 mRNA sequence but lack introns. Based on these features we propose that these are processed genes. Of the L7 genes described here only one (L7- 16b ) exhibits a high degree of homology with L7 mRNA and contains introns. We discuss the possibility that this low representation of intron containing L7 genes may reflect the proportion of functional L7 genes in this multigene family.

Genetic and biochemical distinction among Chinese hamster cell emtA, emtB, and emtC mutants

Genetic and biochemical experiments have enabled us to more clearly distinguish three genetic loci, emtA, emtB, and emtC, all of which can be altered to give rise to resistance to the protein synthesis inhibitor, emetine, in cultured Chinese hamster cells. Genetic experiments have demonstrated that, unlike the emtB locus, neither the emtA locus nor the emtC locus is linked to chromosome 2 in Chinese hamster cells, clearly distinguishing the latter two genes from emtB. emtA mutants can also be distinguished, biochemically, from emtB and emtC mutants based upon different degrees of cross-resistance to another inhibitor of protein synthesis, cryptopleurine. Two-dimensional gel electrophoretic analysis of ribosomal proteins failed to detect any electrophoretic alterations in ribosomal proteins from emtA or emtC mutants that could be correlated with emetine resistance. However, a distinct electrophoretic alteration in ribosomal protein S14 was observed in an emtB mutant. In addition, the parental Chinese hamster peritoneal cell line of an emtC mutant, and the emtC mutant itself, are apparently heterozygous for an electrophoretic alteration in ribosomal protein L9.

Somatic cell genetics and gene families

The utility of somatic cell genetic analysis for the chromosomal localization of genes in mammals is well established. With the development of recombinant DNA probes and efficient blotting techniques that allow visualization of single-copy cellular genes, somatic cell genetics has been extended from the level of phenotypes expressed by whole cells to the level of the cellular genome itself. This extension has proved invaluable for the analysis of genes not readily expressed in somatic cell hybrids and for the study of multigene families, especially pseudogenes dispersed in different chromosomes throughout the genome.

Construction and characterization of Chinese hamster cell EmtA EmtB double mutants

Starting with hybrid cell lines between a Chinese hamster cell EmtA mutant and a Chinese hamster cell EmtB mutant, we have constructed cell lines that are homozygous for mutant alleles at both the emtA locus and the emtB locus, by using a two-step segregation protocol. The EmtA EmtB double mutants are approximately 10-fold more resistant to emetine inhibition than either of the parental mutants. Having both the EmtA mutation and the EmtB mutation expressed in the same cell also results in a level of resistance to cryptopleurine that is significantly higher than a simple additive effect of the two mutations alone. Analysis of ribosomal proteins by two-dimensional polyacrylamide gel electrophoresis demonstrated that a parental hybrid and a first-step segregant, which has lost the wild-type emtA allele, synthesize both a normal and an altered form of ribosomal protein S14, whereas an EmtA EmtB double mutant synthesizes only the altered form of this ribosomal protein. This result confirms that the emtB locus is the structural gene for ribosomal protein S14. Our results also suggest that the products of the emtA and emtB loci interact directly, indicating that the emtA locus, like the emtB locus, encodes a component of the ribosome.

Construction and characterization of Chinese hamster cell EmtA EmtB double mutants

Starting with hybrid cell lines between a Chinese hamster cell EmtA mutant and a Chinese hamster cell EmtB mutant, we have constructed cell lines that are homozygous for mutant alleles at both the emtA locus and the emtB locus, by using a two-step segregation protocol. The EmtA EmtB double mutants are approximately 10-fold more resistant to emetine inhibition than either of the parental mutants. Having both the EmtA mutation and the EmtB mutation expressed in the same cell also results in a level of resistance to cryptopleurine that is significantly higher than a simple additive effect of the two mutations alone. Analysis of ribosomal proteins by two-dimensional polyacrylamide gel electrophoresis demonstrated that a parental hybrid and a first-step segregant, which has lost the wild-type emtA allele, synthesize both a normal and an altered form of ribosomal protein S14, whereas an EmtA EmtB double mutant synthesizes only the altered form of this ribosomal protein. This result confirms that the emtB locus is the structural gene for ribosomal protein S14. Our results also suggest that the products of the emtA and emtB loci interact directly, indicating that the emtA locus, like the emtB locus, encodes a component of the ribosome.

Genetic and biochemical distinction among Chinese hamster cell emtA, emtB, and emtC mutants

Genetic and biochemical experiments have enabled us to more clearly distinguish three genetic loci, emtA, emtB, and emtC, all of which can be altered to give rise to resistance to the protein synthesis inhibitor, emetine, in cultured Chinese hamster cells. Genetic experiments have demonstrated that, unlike the emtB locus, neither the emtA locus nor the emtC locus is linked to chromosome 2 in Chinese hamster cells, clearly distinguishing the latter two genes from emtB. emtA mutants can also be distinguished, biochemically, from emtB and emtC mutants based upon different degrees of cross-resistance to another inhibitor of protein synthesis, cryptopleurine. Two-dimensional gel electrophoretic analysis of ribosomal proteins failed to detect any electrophoretic alterations in ribosomal proteins from emtA or emtC mutants that could be correlated with emetine resistance. However, a distinct electrophoretic alteration in ribosomal protein S14 was observed in an emtB mutant. In addition, the parental Chinese hamster peritoneal cell line of an emtC mutant, and the emtC mutant itself, are apparently heterozygous for an electrophoretic alteration in ribosomal protein L9.

Molecular cloning and analysis of the CRY1 gene: a yeast ribosomal protein gene

Using cloned DNA from the vicinity of the yeast mating type locus (MAT) as a probe, the wild type allele of the cryptopleurine resistance gene CRY1 has been isolated by the technique of chromosome walking and has been shown to be identical to the gene for ribosomal protein 59. A recessive cryR1 allele has also been cloned, using the integration excision method. The genetic distance from MAT to CRY1 is 2.2 cM, while the physical distance is 21 kb, giving a ratio of about 10 kb/cM for this interval. The phenotypic expression of both plasmid borne alleles of the gene can be detected in vivo. The use of this gene as a hybridization probe to examine RNA processing defects in the rna 2, rna 3, rna 4, rna 8, and rna 11 mutants is also discussed.

Detection and localization of a class of proteins immunologically related to a 100-kDa nucleolar protein

A high-molecular-mass nucleolar protein (100-kDa protein) is associated with nascent pre-rRNA and pre-ribosomes in Chinese hamster ovary cells. We have prepared antiserum against the 100-kDa protein and we have used it to study the intracellular localization and the possible processing of this protein. Serologically related proteins were detected in the nucleolus and in ribosomes. Proteins of various subcellular fractions were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, transferred to nitrocellulose filters, reacted with serum and the protein-immunoglobulin complexes were revealed by 125I-labeled protein A. In the nucleolus, four proteins with molecular masses of 100 kDa, 95 kDa, 76 kDa and 70 kDa were thus visualized. In the ribosomes, two proteins (of 100 kDa and 76 kDa) gave a strong reaction while six others (of 70 kDa, 60 kDa, 50 kDa, 30 kDa, 21 kDa, 18 kDa) reacted slightly. By immunological precipitation of total cell extracts, we have shown that the 100-kDa protein antiserum cross-reacts with five proteins with molecular masses of 120 kDa, 100 kDa, 95 kDa, 70 kDa and 60 kDa. Specific degradation of the 100-kDa protein into similar peptides with molecular masses of 95 kDa, 76 kDa, 70 kDa, 60 kDa and 50 kDa can be achieved by incubation of isolated nucleoli or of purified 100-kDa protein in vitro. Cleavage of the protein is due to a thiol endoprotease which is tightly bound to the 100-kDa protein. Possible relations between the maturation of this preribosomal protein into ribosomal proteins and the processing of preribosomal RNA into mature ribosomal RNA are discussed.

Ribosomal proteins are synthesized preferentially in cells commencing growth

Mouse 3T3 cells, in stationary phase because of serum deprivation, have only half the ribosome content of growing cells. Furthermore, the proportion of protein synthesis devoted to ribosomal proteins is only half that in growing cells. On addition of serum the synthesis of each ribosomal protein increases threefold, demonstrating the coordination of the synthesis of the ribosomal proteins. Half that increase is due to a general increase in total protein synthesis; half is due to a differential increase in ribosomal protein synthesis. The latter is abolished by a concentration of actinomycin D which blocks only ribosomal RNA transcription. The results are discussed with reference to a general hypothesis of growth regulation proposed by Stanners et al. (1979).

Isolation of a cloned DNA segment containing a ribosomal protein gene of Drosophila melanogaster

A Drosophila genomic DNA library in the vector Charon 4 was screened using cDNA derived from the small (6S-12S) poly(A)+ mRNA of 2-6-h-old Drosophila embryos. This fraction of mRNA is enriched for ribosomal protein-coding sequences. The selected recombinants were hybridized to total mRNA under conditions which allowed for isolation of homologous mRNAs. The mRNA from these RNA/DNA hybrids was eluted and translated in vitro. The translation products were analyzed by one- and two-dimensional electrophoresis with authentic ribosomal proteins as standards. One cloned DNA segment was found to contain a ribosomal protein gene, and a sequence which hybridizes strongly to at least 5 other ribosomal protein mRNAs.

Yeast use translational control to compensate for extra copies of a ribosomal protein gene

The efficient assembly of ribosomes requires a balanced synthesis of ribosomal RNA and each ribosomal protein. In an attempt to establish the mechanisms responsible for such balanced synthesis we have altered the gene dosage for one of the components by introducing into yeast an autonomously replicating plasmid containing the gene tcm1, which codes for ribosomal protein L3. The plasmid is maintained at 5-10 copies per cell by selection for expression of its URA3 gene. The plasmid-containing cells transcribe 7.5 times as much L3 mRNA as control cells, maintain 3.5 times as much L3 mRNA as control cells and synthesize no more than 1.2 times as much L3 protein as control cells. We conclude that the balanced synthesis of ribosomal proteins is maintained by modulating both the efficiency of translation and the lifetime of their mRNAs.