A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes

Ribosomal protein S19 expression during erythroid differentiation

The gene encoding ribosomal protein S19 (RPS19) has been shown to be mutated in 25% of the patients affected by Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia. As the role of RPS19 in erythropoiesis is still to be defined, we performed studies on RPS19 expression during terminal erythroid differentiation. Comparative analysis of the genomic sequences of human and mouse RPS19 genes enabled the identification of 4 conserved sequence elements in the 5' region. Characterization of transcriptional elements allowed the identification of the promoter in the human RPS19 gene and the localization of a strong regulatory element in the third conserved sequence element. By Northern blot and Western blot analyses of murine splenic erythroblasts infected with the anemia-inducing strain Friend virus (FAV cells), RPS19 mRNA and protein expression were shown to decrease during terminal erythroid differentiation. We anticipate that these findings will contribute to further development of our understanding of the contribution of RPS19 to erythropoiesis.

Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions

Various portions of the region surrounding the site where two ancestral chromosomes fused to form human chromosome 2 are duplicated elsewhere in the human genome, primarily in subtelomeric and pericentromeric locations. At least 24 potentially functional genes and 16 pseudogenes reside in the 614-kb of sequence surrounding the fusion site and paralogous segments on other chromosomes. By comparing the sequences of genomic copies and transcripts, we show that at least 18 of the genes in these paralogous regions are transcriptionally active. Among these genes are new members of the cobalamin synthetase W domain (CBWD) and forkhead domain FOXD4 gene families. Copies of RPL23A and SNRPA1 on chromosome 2 are retrotransposed-processed pseudogenes that were included in segmental duplications; we find 53 RPL23A pseudogenes in the human genome and map the functional copy of SNRPA1 to 15qter. The draft sequence of the human genome also provides new information on the location and intron-exon structure of functional copies of other 2q-fusion genes (PGM5, retina-specific F379, helicase CHLR1, and acrosin). This study illustrates that the duplication and rearrangement of subtelomeric and pericentromeric regions have functional relevance to human biology; these processes can change gene dosage and/or generate genes with new functions.

Cloning, expression, and chromosome mapping of the murine Hip/Rpl29 gene

We previously have identified murine heparin/heparan sulfate-interacting protein (HIP) identical to mouse ribosomal protein L29 that is, like its human orthologue, distinctively expressed both on the cell surface and intracellularly in different adult tissues and cell types. In the present study, we show that mouse HIP/RPL29 is encoded by a single mRNA and that it is expressed to different extents in most of the tissues of the developing embryo without restriction to a specific cell type. We isolated the single-copy gene coding for murine Hip/Rpl29 among a large number of pseudogenes, established its structure, and assigned its location to distal chromosome 9. Similar to other ribosomal protein promoters, the promoter of Hip/Rpl29 is rich in polypyrimidine tracts, contains binding motifs for ubiquitously expressed transcription factors, and lacks a TATA box. Progressive 5' deletion analyses identified a strong enhancer region that includes CT-rich sequences and a potential consensus binding site for NF-kappaB. These data will provide valuable tools to progress the understanding of HIP/RPL29 function as a ribosomal protein and/or as a regulator of growth and cell adhesion through interaction with heparan sulfate proteoglycans.

Genomic structure and expression of the murine Hmgi(y) gene

Mammalian HMGI proteins belong to the high mobility group (HMG) of small non-histone nuclear proteins, and function as architectural factors to mediate structural changes in DNA. The HMGI family consists of three members: HMGI, HMGY and HMGI-C. As pseudogenes have complicated the genomic analysis of murine Hmgi(y), a mouse lambda FIX II genomic library was screened with an intron-specific probe to identify and characterize the authentic Hmgi(y) gene. The murine Hmgi(y) gene is 7.2kb long and contains four protein coding exons and two additional exons encoding part of the 5' untranslated region. Sequencing confirms that an alternative splicing site within exon 3 results in the two protein isoforms: Hmgi and Hmgy. Primer extension experiments revealed that at least three transcription start sites exist in the 5' end of the gene. It has been well established that the expression of both Hmgi-c and Hmgi(y) is readily detectable throughout embryogenesis. Unlike Hmgi-c, whose expression is restricted to embryogenesis, a Northern hybridization analysis showed low-level expression of Hmgi(y) in adult mouse tissues. Similarly, when tissues from newborn animals were examined, Hmgi(y) expression was readily detected at a level of intensity intermediate between that found in embryos and adults. Understanding the gene structure and expression pattern will provide important insights into the in-vivo function of Hmgi(y).

Isolation, structural analysis and mapping of the functional gene of human ribosomal protein S26

The nucleotide sequence of the gene of human ribosomal protein S26 has been assembled from cDNA and genomic PCR-amplified DNA fragments, and its transcription start site has been determined by primer extension. The gene is composed of four exons and three introns spanning 2027bp. Like other ribosomal protein genes of vertebrates, this gene contains a short first exon corresponding exactly to the short untranslated 5'- UTR. Its transcription start site is embedded in a polypyrimidine tract. Using PCR on DNAs from hybrid cell lines with a different set of human chromosomes, the intron-containing gene of ribosomal protein S26 was mapped to human chromosome 12.

A map of 75 human ribosomal protein genes

We mapped 75 genes that collectively encode >90% of the proteins found in human ribosomes. Because localization of ribosomal protein genes (rp genes) is complicated by the existence of processed pseudogenes, multiple strategies were devised to identify PCR-detectable sequence-tagged sites (STSs) at introns. In some cases we exploited specific, pre-existing information about the intron/exon structure of a given human rp gene or its homolog in another vertebrate. When such information was unavailable, selection of PCR primer pairs was guided by general insights gleaned from analysis of all mammalian rp genes whose intron/exon structures have been published. For many genes, PCR amplification of introns was facilitated by use of YAC pool DNAs rather than total human genomic DNA as templates. We then assigned the rp gene STSs to individual human chromosomes by typing human-rodent hybrid cell lines. The genes were placed more precisely on the physical map of the human genome by typing of radiation hybrids or screening YAC libraries. Fifty-one previously unmapped rp genes were localized, and 24 previously reported rp gene localizations were confirmed, refined, or corrected. Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes. Chromosome 19, known to have a high gene density, contains an unusually large number of rp genes (12). This map provides a foundation for the study of the possible roles of ribosomal protein deficiencies in chromosomal and Mendelian disorders.

Mapping of the human ribosomal large subunit protein gene RPL29 to human chromosome 3q29-qter

The human ribosomal protein L29, which we reported previously, was subsequently shown to have the same nucleotide sequence as that of cell surface heparin/heparan sulfate-binding protein, designated HP/HS interacting protein. A polymerase chain reaction-based strategy was used to distinguish the functional intron-containing gene RPL29 (HGMW-approved symbol) from multiple pseudogenes. By somatic cell hybrid analysis, radiation hybrid mapping, and fluorescence in situ hybridization, we have located RPL29 on the telomeric region of the q arm of chromosome 3. RPL29 is the most distal marker of the long armof chromosome 3. Of the human ribosomal protein genes mapped, RPL29 is the shortest distance from another ribosomal protein gene marker, RPL35 a which has also been mapped to the 3q29-qter region.

Southern hybridization analyses of somatic cell hybrids reveal that human BB1 is a member of a multigene family dispersed throughout the human genome and appears to be linked to the human G25K genes

The hBB1 RNA (2.3 kb in length) encodes a 57-amino-acid protein whose production is essential for cellular transit of G1 phase of the cell cycle (Moats-Staats et al., 1994). Homology searches of GenBank and EMBL revealed that bases 1-234 of the hBB1 cDNA were 97% homologous to the 3' terminal 234 bases of the g25K cDNA (bases 940-1,175, Shinjo et al., 1990) the human homolog of the yeast cdc42 cDNA. We have used the techniques of the long-range polymerase chain reaction (PCR) (Barnes, 1994) and Southern hybridization analyses of a somatic cell hybrid panel to investigate hBB1 gene structure and to determine whether the hBB1 gene(s) overlaps the g25K gene. These studies have demonstrated that the hBB1 RNA is encoded by a gene family composed of eight members that is dispersed throughout the human genome localizing under high-stringency conditions to chromosomes 1, 4, 7, 8, and 20. We have also determined that two hBB1 gene(s) and two g25K gene(s) map to similar-size Bam HI restriction fragments on chromosomes 4 and 7.

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.

The L19 ribosomal protein gene (RPL19): gene organization, chromosomal mapping, and novel promoter region

The intron-containing genes encoding rat and human ribosomal protein L19 (RPL19) have been cloned. The DNA sequences of the entire rat RPL19 gene and the 5' end of the human RPL19 gene have been determined. Sequence comparison of corresponding regions of the two genes reveals a striking interspecies homology in the 5' upstream region, outside the transcribed and coding regions. The transcriptional start sites of the two genes have been determined and are identical. Both rat and human RPL19 genes have 5' ends associated with CpG islands. A promoter deletion analysis of the rat RPL19 gene suggests that this promoter may differ from those of all previously characterized ribosomal protein genes in requiring far upstream sequences for efficient gene expression. By fluorescence in situ hybridization analysis, the position of the human RPL19 gene has been sublocalized to 17q11 and may be coamplified with the erbB-2 gene in human breast cancer cells. The similarities and differences between RPL19 and other previously characterized ribosomal protein genes are discussed.

An S18 ribosomal protein gene copy at the Arabidopsis PFL locus affects plant development by its specific expression in meristems

In Arabidopsis, mutation at PFL causes pointed first leaves, reduced fresh weight and growth retardation. We have cloned the wild-type PFL gene by T-DNA tagging, and demonstrate that it complements the mutant phenotype. PFL codes for ribosomal protein S18, based on the high homology with rat S18 and on purification of S18-equivalent peptides from plant ribosomes. pfl represents the first mutation in eukaryotic S18 proteins or their S13 prokaryotic counterparts, involved in translation initiation. Arabidopsis contains three S18 gene copies dispersed in the genetic map; they are all transcribed and code for completely identical proteins. No transcript is detected from the mutated gene, S18A. The activity of the S18A promoter is restricted to meristems, with a markedly high expression at the embryonic heart stage, and to wounding sites. This means that plants activate an extra copy of this ribosomal protein gene in tissues with cell division activity. We postulate that in meristematic tissues plants use transcriptional control to synthesize extra ribosomes to increase translational efficiency. In analogy with this, an additional, developmentally regulated gene copy might be expected for all ribosomal proteins.

Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes

The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.

Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes

The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.

The mammalian genome shaping activity of reverse transcriptase

Reverse transcriptase catalyses the conversion of RNA into DNA. This operation seems to have largely contributed to the evolution of complex genomes. More than 10% of a mammalian genome is composed of sequences with reverse transcribed origin, most of which consists of repeated sequences (SINEs, LINEs). In spite of their simplicity, these sequences can play a key role in evolution by favoring illegitimate recombination. In addition to this abundant material, retrotransposed sequences include retrotransposons, retroviruses and genes depleted from intervening sequences, known as pseudogenes. Some of these sequences can be functional or involved in the regulation of neighbouring genes. These hallmarks of reverse transcription activity indicate that it has largely contributed to the fluidity of modern genomes.

Two distinct yeast proteins are related to the mammalian ribosomal polypeptide L7

The RLP7 gene of Saccharomyces cerevisiae was cloned, sequenced and localized to the right arm of chromosome XIV, close to the centromere. It encodes a predicted polypeptide (RLP7p) of 322 amino acids, with a calculated molecular mass of 36 kDa and an isoelectric point of 9.6. Putative open reading frames very similar to RLP7 are present in two other yeasts, Kluyveromyces lactis and Candida utilis. The RLP7p gene product has significant sequence similarity to the S. cerevisiae YL8 polypeptide of the large ribosomal subunit (Mizuta et al., 1992), itself homologous to the L7 subunit of mammalian ribosomes. However, RLP7p and YL8 do not functionally replace each other, since an rlp7-delta::HIS3 strain is completely inviable. Judging from its predicted mass, isoelectric point and amino acid sequence, RLP7p does not correspond to any ribosomal component biochemically identified so far in S. cerevisiae, and also differs from all known ribosomal proteins by the low codon usage bias of its gene.

Organization, inducible-expression and chromosome localization of the human HMG-I(Y) nonhistone protein gene

Members of the HMG-I(Y) family of mammalian nonhistone proteins are of importance because they have been demonstrated to bind specifically to the minor groove of A.T-rich sequences both in vitro and in vivo and to function as gene transcriptional regulatory proteins in vivo. Here we report the cloning, sequencing, characterization and chromosomal localization of the human HMG-I(Y) gene. The gene has several potential promoter/enhancer regions, a number of different transcription start sites and numerous alternatively spliced exons making it one of the most complex nonhistone chromatin protein-encoding genes so far reported. The putative promoter/enhancer regions each contain a number of conserved nucleotide sequences for potential binding of inducible regulatory transcription factors. Consistent with the presence of these conserved sequences, we found that transcription of the HMG-I(Y) gene is inducible in human lymphoid cells by factors such as phorbol esters and calcium ionophores. Detailed sequence analysis confirms our earlier suggestion that alternative splicing of precursor mRNAs gives rise to the major HMG-I and HMG-Y isoform proteins found in human cells. Furthermore, the gene's exon-intron arrangement fully accounts for all of the previously cloned human HMG-I(Y) cDNAs (1,2). Also of considerable interest is the fact that each of the three different DNA-binding domain peptides present in an individual HMG-I(Y) protein is coded for by sequences present on separate exons thus potentially allowing for exon 'shuffling' of these functional domains during evolution. And, finally, we localized the gene to the short arm of chromosome 6 (6p) in a region that is known to be involved in rearrangements, translocations and other abnormalities correlated with a number of human cancers.

Identification and genetic mapping of the murine gene and 20 related sequences encoding chromosomal protein HMG-17

HMG-17 is an abundant, nonhistone chromosomal protein that binds preferentially to nucleosomal core particles of mammalian chromatin. The human gene for HMG-17 has been localized to Chromosome (Chr) 1p, but the murine gene has not been previously mapped. Here we identify the murine functional gene, Hmg17, from among more than 25 related sequences (probably processed pseudogenes) and show that it is located on mouse Chr 4, in a region known to have conserved linkage relationships with human Chr 1p. We also report the map locations of 20 additional Hmg17-related sequences on mouse Chrs 1, 2, 3, 5, 7, 8, 9, 13, 15, 16, 17, 18, and X. The multiple, dispersed members of the Hmg17 multigene family can be detected efficiently with a single cDNA probe and provide useful markers for genetic mapping studies in mice.

Conservation of the organization of five tightly clustered genes over 600 million years of divergent evolution

The organization of the mouse surfeit locus is unusual in that it contains six housekeeping genes (Surf-1-Surf-6), which are unrelated by sequence homology, in the tightest mammalian gene cluster thus far described. A maximum of only 73 base pairs separates any two of the four well-characterized genes, and two of the genes overlap at their 3' ends. The direction of transcription of each of the five surfeit genes, Surf-1-Surf-5, alternates with respect to that of its neighbor, suggesting cis-interaction or coregulation between the genes by mechanisms such as the sharing of regulatory elements and/or antisense regulation. The Surf-3 gene has been identified as encoding the ribosomal protein L7a (Rpl7a). We have used the high conservation of the Rpl7a gene to clone the chicken gene and surrounding genomic DNA. The tight clustering and juxtaposition of at least five of the surfeit genes (Surf-1-Surf-5) and their associated CpG-rich islands have been found to be conserved over the 600 million years of divergent evolution that separates birds and mammals. This strongly suggests that the surfeit locus represents a different form of gene cluster in which gene organization may play both a positive and negative regulatory role in gene expression possibly via cis-interactions between the closely spaced genes.

Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds

The transcriptional initiation sites of the chicken ribosomal protein L7a (rpL7a) gene have been determined and found to occur at three consecutive cytidine residues at the start of a polypyrimidine tract of 8 base pairs (bp). A comparative analysis of the 5' upstream regions of the mouse, human and chicken rpL7a genes identified two sequence elements (Box A and Box B) conserved over the 600 million years of divergent evolution that separate mammals and birds. Only Box A (nts - 56 to - 39) and Box B (nts - 25 to - 4) sequences were detected to bind nuclear factors from mouse nuclear extracts in an analysis of the mouse rpL7a 5' upstream sequence. Box A and Box B bind different nuclear factors and the factor binding to mouse Box A and mouse Box B sequences could be effectively competed by corresponding homologous sequences from the human and chicken rpL7a promoters. These results indicate that elements of the rpL7a promoter region are conserved between mammals and birds. An in vivo analysis of the mouse rpL7a 5' upstream sequence required for efficient transcription identified the 5' border of the minimal promoter region as lying between nts - 50 and - 56. Constructs containing 56 bp of 5' upstream DNA and the first 25 bp rpL7a exon were very efficiently transcribed indicating that sequences within the first intron are not required for gene expression. No sequence similarity was detected between the rpL7a promoter elements and described promoter elements of other eukaryotic ribosomal protein genes.

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.

Germ cell-specific expression of a gene encoding eukaryotic translation elongation factor 1 alpha (eEF-1 alpha) and generation of eEF-1 alpha retropseudogenes in Xenopus laevis

We have studied by in situ hybridization the expression of the genes encoding the somatic form and the oocyte form of Xenopus laevis eEF-1 alpha. The somatic form of eEF-1 alpha (eEF-1 alpha S) mRNA is virtually undetectable in male and female germ cells of the adult gonad but is very abundant in embryonic cells after the neurula stage. In contrast, another form of eEF-1 alpha (eEF-1 alpha O) mRNA is highly concentrated in oogonia and in previtellogenic oocytes but is undetectable in eggs and embryos. eEF-1 alpha O mRNA is also present in spermatogonia and spermatocytes of adult testis. The latter finding identifies eEF-1 alpha O mRNA as a germ cell-specific gene product. Although germ cells contain very little eEF-1 alpha S mRNA, several eEF-1 alpha S retropseudogenes exist in X. laevis chromosomes. These genes are thought to arise in germ cells from reverse transcription of mRNA and subsequent integration of the cDNA copies into chromosomal DNA. We suggest that eEF-1 alpha S pseudogenes are generated in primordial germ cells of the embryo before they differentiate into oogonia or spermatogonia.

The structure of a gene containing introns and encoding rat ribosomal protein P2

The single rat ribosomal protein P2 gene containing introns has been characterized. It has 2275 nucleotides distributed in 5 exons and 4 introns. The sequence of amino acids encoded in the exons corresponds exactly to that derived before from a cDNA. Only this one P2 gene in a family of approximately 9 members has introns and is expressed. There are two transcriptional start sites (adjacent cytidine residues) located in a tract of 10 pyrimidines flanked by GC-rich regions. The P2 gene, like other mammalian ribosomal protein genes, lacks a TATA box; however, it has at positions -30 to -27 the sequence TTTA which may be a degenerate TATA box and may serve the same function. The architecture of the P2 gene, and especially the structure of the promoter region, resembles that of other mammalian ribosomal protein genes. This suggests that the common features contribute to the coordinate regulation of their transcription and that the stoichiometry of P2 (it is present in 2 copies in the ribosome) is achieved by regulation of the translation of its mRNA.

The organization and expression of the Saccharomyces cerevisiae L4 ribosomal protein genes and their identification as the homologues of the mammalian ribosomal protein gene L7a

A cDNA for the mouse ribosomal protein (rp) L7a, formerly called Surf-3, was used as a probe to isolate two homologous genes from Saccharomyces cerevisiae. The two yeast genes (L4-1 and L4-2) were identified as encoding S. cerevisiae L4 by 2D gel analysis of the product of the in vitro translation of hybrid-selected mRNA and additionally by direct amino acid sequencing. The DNA sequences of the two yeast genes were highly homologous (95%) over the 771 bp that encode the 256 amino acids of the coding regions but showed little homology outside the coding region. L4-1 differed from L4-2 by 7 out of the 256 amino acids in the coding region, which is the greatest divergence between the products of any two duplicated yeast ribosomal protein genes so far reported. There is strong homology between the mouse rpL7a/Surf-3 and the yeast L4 genes -57% at the nucleic acid level and also 57% at the amino acid level (though some regions reach as much as 80-90% homology). While most yeast ribosomal protein genes contain an intron in their 5' region both L4-1 and L4-2 are intronless. The mRNAs derived from each yeast gene contained heterogenous 5' and 3' ends but in each case the untranslated leaders were short. The L4-1 mRNA was found to be much more abundant than the L4-2 mRNA as assessed by cDNA and transcription analyses. Yeast cells containing a disruption of the L4-1 gene formed much smaller colonies than either wild-type or disrupted L4-2 strains. Disruption of both L4 genes is a lethal event, probably due to an inability to produce functional ribosomes.

A phage screening method to isolate intron-containing genes in the presence of multiple processed pseudogenes

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The primary structure of rat ribosomal protein S16

The amino acid sequence of rat ribosomal protein S16 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2-terminal amino acid sequence of the protein. S16 contains 145 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular mass of 16,304. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 11-13 copies of the S16 gene. The mRNA for the protein is about 700 nucleotides in length. Rat S16 is homologous to mouse S16 (there are 2 amino acid changes and a residue is deleted) and related to Halobacterium morismortui ribosomal protein S3 and to Escherichia coli S9.