Functional analysis of human RPS14 null alleles.

Previously we described a large collection of cloned human DNAs that encode chemically defined missense mutations within the ribosomal protein S14 sequence. We determined that biologically inactive (i.e. null) alleles resulted primarily from point mutations targeted to two internal segments of the S14-coding sequence and designated these functionally critical regions as domains B and D. Further, we inferred that structural determinants within domains B and D are required for proper incorporation of the S14 protein into nascent 40 S ribosomal particles and/or for the normal function of mature cytoplasmic ribosomes. In this study we have used immunofluorescence to monitor the intracellular trafficking of epitopically labeled human S14 protein isoforms transiently expressed by cultured Chinese hamster cells. Data obtained distinguish null alleles of RPS14 which encode proteins that are not incorporated into pre-ribosomal subunit particles from null alleles whose products are compatible with normal ribosome assembly processes but result in functionally inactive cytoplasmic 40 S ribosomal subunits. Mutations assigned to the first allele class involve amino acid replacements located within S14 domains B and D; whereas mutations assigned to the second class are distributed throughout the S14 protein-coding sequence.

The gene encoding human ribosomal protein S24 and tissue-specific expression of differentially spliced mRNAs.

Starting with a cloned cDNA encoding human ribosomal protein S24 [Brown et al., Gene 91 (1990) 293-296], we PCR-amplified two introns from the human RPS24 locus. These then were used as unique nucleic-acid probes to isolate a 12-kb RPS24 gene fragment from a library of human genomic DNA. The nucleotide sequence of human RPS24 (4942 bp), its exon-intron organization and mRNA transcription start point were determined using standard procedures. RT-PCR analyses of S24 mRNAs from multiple human tissues and cell lines revealed two mRNA isoforms which differ from each other, as well as murine S24 mRNAs due to alternative exon splices near the 3' end of the gene.

A densely methylated DNA island is associated with a chromosomal replication origin in the human RPS14 locus.

We describe a 258-bp densely methylated DNA island (DMI) and chromosomal origin of bidirectional DNA replication within the transcribed portion of the human RPS14 intron 1. Together with the DMIs previously detected in two functional Chinese hamster replication origins [see Ref. 1, pp. 5636-5644], observations described in this report strengthen the correlation between densely methylated DNA islands and active mammalian chromosomal replication origins. Accordingly, DMIs may prove to be reliable physical markers for origins of bidirectional DNA replication in complex genomic DNAs of higher animals.

Regulation of human RPS14 transcription by intronic antisense RNAs and ribosomal protein S14.

RNase protection studies reveal two stable RNAs (250 and 280 nucleotides) transcribed from the antisense strand of the human ribosomal protein gene RPS14's first intron. These transcripts, designated alpha-250 and alpha-280, map to overlapping segments of the intron's 5' sequence. Neither RNA encodes a polypeptide sequence, and both are expressed in all human cells and tissues examined. Although alpha-280 is detected among both the cells' nuclear and cytoplasmic RNAs, the great majority of alpha-250 is found in the cytoplasmic subcellular compartment. As judged by its resistance to high concentrations of alpha-amanitin, cell-free transcription of alpha-250 and alpha-280 appears to involve RNA polymerase I. Tissue culture transfection and cell-free transcription experiments demonstrate that alpha-250 and alpha-280 stimulate S14 mRNA transcription, whereas free ribosomal protein S14 inhibits it. Electrophoretic mobility shift experiments indicate specific binary molecular interactions between r-protein S14, its message and the antisense RNAs. In light of these data, we propose a model for fine regulation of human RPS14 transcription that involves RPS14 intron 1 antisense RNAs as positive effectors and S14 protein as a negative effector.

A mammalian origin of bidirectional DNA replication within the Chinese hamster RPS14 locus.

Two complementary experimental approaches have been used to identify a chromosomal origin of bidirectional DNA replication within or immediately downstream of the Chinese hamster ribosomal protein S14 gene (RPS14). The replication origin, designated oriS14, maps within a 1.6- to 2.0-kbp region of RPS14 that includes the gene's third and fourth introns, exons IV plus V, and approximately 500 bp of proximal downstream flanking DNA. The nucleic acid sequence encoding oriS14 closely resembles the other mammalian chromosomal replication origins whose primary structures are known. It contains DNA binding sites for a large number of transcription factors, replication proteins, and mammalian oncogenes as well as several dinucleotide repeat motifs, an AT-rich region, and a sequence that is likely to bend the DNA. In contrast to the other well-characterized mammalian replication origins, which are autosomal and therefore carried as two copies per somatic cell, oriS14 is encoded by single-copy DNA within a hemizygous segment of chromosome 2q in CHO-K1 cells. Also, other known mammalian replication origins are situated in nontranscribed, intergenic DNA, whereas the DNA sequence encoding oriS14 substantially overlaps the transcribed portion of a constitutively expressed housekeeping gene.

Densely methylated DNA islands in mammalian chromosomal replication origins.

Densely methylated DNA sequence islands, designated DMIs, have been observed in two Chinese hamster cell chromosomal replication origins by using a PCR-based chemical method of detection. One of the origins, oriS14, is located within or adjacent to the coding sequence for ribosomal protein S14 on chromosome 2q, and the other, ori-beta, is approximately 17 kbp downstream of the dhfr (dihydrofolic acid reductase) locus on chromosome 2p. The DMI in oriS14 is 127 bp long, and the DMI in ori-beta is 516 bp long. Both DMIs are bilaterally methylated (i.e., all dCs are modified to 5-methyl dC) only in cells that are replicating their DNA. When cell growth and DNA replication are arrested, methylation of CpA, CpT, and CpC dinucleotides is lost and the sequence islands display only a subset of their originally methylated CpG dinucleotides. Several possible roles for DMI-mediated regulation of mammalian chromosomal origins are considered.

Multiple regulatory elements ensure accurate transcription of a human ribosomal protein gene.

Previously we have shown that expression of a cloned human ribosomal protein gene, RPS14, depends upon regulatory sites located within the gene's proximal upstream DNA plus its first intron. In order to identify cis-active sequence motifs within the RPS14 promoter-enhancer complex, we transiently expressed a set of informative deletion clones in cultured Chinese hamster ovary cells. These experiments revealed three DNA sequence motifs that surround the S14 mRNA initiation site and are necessary for accurate transcription. Electrophoretic mobility shift, DNase I footprint, and methylation interference assays resolved two nuclear proteins, NF alpha-1 and NF beta-1, which bind specifically to these regulatory motifs. NF-alpha 1 recognizes a pair of 6-bp target motifs (5'-TTCCGG-3') that flank the 5' end of RPS14 exon I; and NF-beta 1 binds to a 10-bp target sequence (5'-CCGTGGGAAC-3') within the gene's first intron. Site-directed deletion mutations within the NF-alpha 1 and -beta 1 binding sites markedly inhibit S14 mRNA transcription.

Deoxycytidine methylation and the origin of spontaneous transition mutations in mammalian cells.

Previously we described a recurrent, site-specific G4784 --> A transition mutation affecting exon V of the Chinese hamster ovary cell RPS14 gene. Because the mutation is located within a CpG dinucleotide, we considered the possibility that deoxycytidine methylation might be responsible for the transition's unusually high frequency and site specificity. Therefore, we used a procedure based on the PCR amplification of bisulfite-modified genomic DNA to analyze the pattern of DNA cytosine methylation in exon V of the CHO cell RPS14 locus. Our data indicate that the CpG dinucleotide targeted by the transition mutation is stably methylated in CHO cell chromosomes. This finding supports the notion that deoxycytidine methylation promotes "spontaneous", site-specific transition mutations in mammalian cells.

Fine-structure map of the human ribosomal protein gene RPS14.

We have used polymerase chain reaction-mediated chemical mutagenesis (J.-J. Diaz, D. D. Rhoads, and D. J. Roufa, BioTechniques 11:204-211, 1991) to analyze the genetic fine structure of a human ribosomal protein gene, RPS14. Eighty-three DNA clones containing 158 random single-base substitution mutations were isolated. Mutant RPS14 alleles were tested for biological activity by transfection into cultured Chinese hamster cells. The resulting data permitted us to construct a map of the S14-coding sequence that is comparable to available fine-structure genetic maps of many prokaryotic and lower eukaryotic gene loci. As predicted from the multiplicity of protein-protein and protein-RNA interactions required for ribosomal protein transport and assembly into functional ribosomal subunits, the distribution of null mutations indicated that S14 is composed of multiple, functionally distinct polypeptide domains. Two of the protein's internal domains, designated domains B and D, were essential for S14 biological activity. In contrast, mutations which altered or deleted S14's amino-terminal 20 amino acid residues (domain A) had no observable effect on the protein's assembly and function in mammalian ribosomes. Interestingly, S14 structural domains deduced by in vitro mutagenesis correlate well with the RPS14 gene's exon boundaries.

PCR-mediated chemical mutagenesis of cloned duplex DNAs.

We describe an efficient, PCR-mediated protocol for random chemical mutagenesis of cloned duplex DNAs. The method involves a single molecular cloning step and is compatible with a wide variety of recombinant DNA vectors. To illustrate the procedure, we report the nitrous acid mutagenesis of a human ribosomal protein S14 cDNA fragment.

Molecular evolution of the mammalian ribosomal protein gene, RPS14.

Ribosomal protein S14 genes (RPS14) in eukaryotic species from protozoa to primates exhibit dramatically different intron-exon structures yet share homologous polypeptide-coding sequences. To recognize common features of RPS14 gene architectures in closely related mammalian species and to evaluate similarities in their noncoding DNA sequences, we isolated the intron-containing S14 locus from Chinese hamster ovary (CHO) cell DNA by using a PCR strategy and compared it with human RPS14. We found that rodent and primate S14 genes are composed of identical protein-coding exons interrupted by introns at four conserved DNA sites. However, the structures of corresponding CHO and human RPS14 introns differ significantly. Nonetheless, individual intron splice donor, splice acceptor, and upstream flanking motifs have been conserved within mammalian S14 homologues as well as within RPS14 gene fragments PCR amplified from other vertebrate genera (birds and bony fish). Our data indicate that noncoding, intronic DNA sequences within highly conserved, single-copy ribosomal protein genes are useful molecular landmarks for phylogenetic analysis of closely related vertebrate species.

Genetic analysis of a vital mammalian housekeeping locus using CHO cells that express a transfected mutant allele.

We describe a novel approach for the isolation of null mutations in a vital Chinese hamster ovary (CHO) cell housekeeping gene. Our experimental strategy required introduction of an expressible DNA clone encoding a recessive emetine-resistance allele of ribosomal protein S14 into wild-type CHO cells. Transgene heterozygote (TGH) cell lines, which harbor multiple emetine-resistance S14 transgenes, survive mutations that inactivate the CHO RPS14 locus by virtue of the transgenes' biological function. Null mutations in RPS14 yield TGH clones that display the transgene's drug-resistance phenotype. A large collection of emetine-resistant clones was isolated from one TGH cell line and shown to consist of three types of S14 mutations: (1) nonsense null mutations in the RPS14 protein coding sequence; (2) missense null mutations that affect S14 amino acid residues that have been conserved stringently during eukaryotic evolution; and (3) a recurrent missense mutation that results in a new, functional RPS14 emetine-resistance allele.

A Drosophila ribosomal protein functions in mammalian cells.

A cDNA expression vector encoding Drosophila ribosomal protein S14 was transfected into cultured Chinese hamster ovary (CHO) cells that harbor a recessive RPS14 emetine resistance mutation. Transformants synthesized the insect mRNA and polypeptide and consequently displayed an emetine-sensitive phenotype. These observations indicate that the insect protein was accurately expressed and correctly assembled into functional mammalian 40S ribosomal subunits.

A cDNA encoding human ribosomal protein S24.

We describe the isolation and nucleotide sequence of a cDNA encoding the human 40S ribosomal subunit protein (r-protein) S24 (Mr 15,425). Human S24 is virtually identical to the r-protein encoded by a cloned Xenopus laevis cDNA previously identified as S19 [Amaldi et al., Gene 17 (1982) 311-316].

Antiribosomal S10 antibodies in humans and MRL/lpr mice with systemic lupus erythematosus.

Autoantibodies directed against a ribosomal small subunit protein of 20,000 molecular weight were found in sera from 5 of 44 patients with systemic lupus erythematosus (11%) and 5 of 48 MRL/lpr mice (10%). This ribosomal protein was identified as S10 on the basis of two-dimensional gel electrophoresis and immunoblotting, as well as immunoblots of the purified S10 protein. The S10 protein antigen was readily extracted from ribosomes at low salt (300 mM KCl) and low magnesium (0.5 mM) concentrations, consistent with the highly exposed location proposed for this protein on the 40S subunit. Anti-S10 antibodies were observed significantly more frequently in lupus sera containing both anti-Sm and antiribosomal P protein antibodies and in MRL/lpr sera with anti-Sm activity, suggesting a linked pattern of autoantibody response. Together with anti-Sm and antiribosomal P protein antibodies, anti-S10 represents a third autoantibody highly specific for lupus in humans and MLR/lpr mice.

The Drosophila melanogaster RPS17 gene encoding ribosomal protein S17.

A human ribosomal protein S17 cDNA [Chen et al., Proc. Natl. Acad. Sci. USA 83 (1986) 6907-6911] was used as heterologous probe to isolate S17 clones from Drosophila genomic and cDNA recombinant libraries. Five S17 genomic clones were recognized; all contained overlapping regions of a single chromosomal site. Subsequently the Drosophila RPS17 gene was mapped by in situ hybridization to chromosome 3L, band 67B1-5. The locus spans approximately 1000 bp of DNA and includes four exons. It is preceded by conventional CAAT and TATA RNA polymerase II promoter motifs. The 131 amino acid protein encoded within Drosophila RPS17 is similar to ribosomal proteins from several other eukaryotes. Comparison of eukaryotic S17 proteins' primary structures as well as the number and location of their genes' intervening sequences suggest that S17 is a relatively recent addition to the ribosomal protein family, probably post-dating divergence of eukaryotes and prokaryotes.

Ribosomal protein S14 is encoded by a pair of highly conserved, adjacent genes on the X chromosome of Drosophila melanogaster.

We describe a Drosophila DNA clone of tandemly duplicated genes encoding an amino acid sequence nearly identical to human ribosomal protein S14 and yeast rp59. Despite their remarkably similar exons, the locations and sizes of introns differ radically among the Drosophila, human, and yeast (Saccharomyces cerevisiae) ribosomal protein genes. Transcripts of both Drosophila RPS14 genes were detected in embryonic and adult tissues and are the same length as mammalian S14 message. Drosophila RPS14 was mapped to region 7C5-9 on the X chromosome. This interval also encodes a previously characterized Minute locus, M(1)7C.

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.

A cloned human ribosomal protein gene functions in rodent cells.

Cloned fragments of human ribosomal protein S14 DNA (RPS14) were transfected into cultured Chinese hamster (CHO) cells. Transient expression assays indicated that DNA with as little as 31 base pairs of upstream flanking sequence was transcribed into a polyadenylated, 650-base mRNA that is largely bound to the polyribosomes. In these respects the exogenous human S14 message appeared to function normally in CHO cells. Interestingly, transcription of human RPS14 did not require the TATA sequence located 26 base pairs upstream of exon 1. Stably transformed clones were selected from cultures of emetine-resistant CHO cells (Emr-2) after transfection with pSV2Neo-human RPS14 constructs. Human RPS14 complemented the mutationally based drug resistance of the Chinese hamster cells, demonstrating that the cloned human ribosomal protein gene is functional in rodent cells. Analysis of transformed cells with different amounts of integrated RPS14 indicated that human S14 mRNA levels are not tightly regulated by CHO cells. In contrast, the steady-state S14 level fluctuated only slightly, if at all, in transformed clones whose S14 message contents differed by more than 30-fold. These data support the conclusion that expression of human RPS14 is regulated, at least partially, posttranscriptionally.