Nucleotide sequence of the L1 ribosomal protein gene of Xenopus laevis: remarkable sequence homology among introns

Molecular cloning and characterization of porcine ribosomal protein L21

Ribosomal protein L21 (RPL21) is a structural component of the 60S subunit of the eukaryotic ribosome. This protein has an important role in protein synthesis and the occurrence of hereditary diseases. Pig is a common laboratory model, however, to the best of our knowledge, its RPL21 gene has not been cloned to date. In this study, we cloned and identified the full-length sequence of the pig RPL21 gene for the first time. In addition, we examined its expression pattern and function by using overexpression or knockdown approaches. As a result, we obtained a 604 bp segment that contains a 483 bp open reading frame encoding 160 amino acids. The pig RPL21 gene is located in the “+” strand of chromosome 11, which spans 2167 bp from 4199792 to 4201958. Pig RPL21 protein has nine strands and two helices in its secondary structure. Pig RPL21 is predominantly expressed in ovary and lung, at lower levels in kidney, small intestine, and skin, and at the lowest levels in heart and liver. Furthermore, RPL21 expression is closely connected with cell proliferation and cell cycle arrest. The results are intended to provide useful information for the further study of pig RPL21.

Polarized distribution of mRNAs encoding a putative LDL receptor adaptor protein, xARH (autosomal recessive hypercholesterolemia) in Xenopus oocytes

The Xenopus homologue of hARH (human autosomal recessive hypercholesterolemia) was identified in a screen for vegetally localized RNAs. xARH contains a N-terminal phosphotyrosine binding (PTB) domain that is 91% identical to that of the human gene, a domain previously shown to bind the LDL receptor family members. Maternal xARH, unlike hARH, is present as two transcripts that differ in their 3' UTRs. The large transcript, xARH-alpha, primarily localizes to the oocyte vegetal cortex. The small transcript, xARH-beta, is not localized. During embryogenesis, xARH RNA is found redistributed in a perinuclear pattern. Similar to hARH, xARH is found in the adult liver, but at low levels compared to oocytes. Downstream of the PTB domain is a conserved clathrin box and a C terminal region 50% identical to that of hARH. Previous in vitro studies from this lab have shown xARH can bind the LDLR as well as the vitellogenin (VTG) receptor. We find that injection of the C terminal region missing the PTB domain significantly reduces the internalization of VTG in early stage oocytes, an event that requires the VTG receptor. The data strongly suggest that xARH encodes an adaptor protein that functions in the essential receptor-mediated endocytosis of nutrients during oogenesis. Because xARH protein is found uniformly distributed along the animal/vegetal axis in oocytes, we propose that the localization of xARH-alpha to the vegetal cortex while xARH-beta remains unlocalized, facilitates the uniform distribution of the protein in this extraordinarily large cell.

La protein is associated with terminal oligopyrimidine mRNAs in actively translating polysomes

La is an abundant, mostly nuclear, RNA-binding protein that interacts with regions rich in pyrimidines. In the nucleus it has a role in the metabolism of several small RNAs. A number of studies, however, indicate that La protein is also implicated in cytoplasmic functions such as translation. The association of La in vivo with endogenous mRNAs engaged with polysomes would support this role, but this point has never been addressed yet. Terminal oligopyrimidine (TOP) mRNAs, which code for ribosomal proteins and other components of the translational apparatus, bear a TOP stretch at the 5' end, which is necessary for the regulation of their translation. La protein can bind the TOP sequence in vitro and activates TOP mRNA translation in vivo. Here we have quantified La protein in the cytoplasm of Xenopus oocytes and embryo cells and have shown in embryo cells that it is associated with actively translating polysomes. Disruption of polysomes by EDTA treatment displaces La in messenger ribonucleoprotein complexes sedimenting at 40-60 S. The results of polysome treatment with either low concentrations of micrococcal nuclease or with high concentrations of salt indicate, respectively, that La association with polysomes is mediated by mRNA and that it is not an integral component of ribosomes. Moreover, the analysis of messenger ribonucleoprotein complexes dissociated from translating polysomes shows that La protein associates with TOP mRNAs in vivo when they are translated, in line with a positive role of La in the translation of this class of mRNAs previously observed in cultured cells.

Complementary DNA analysis, expression and subcellular localization of hnRNP E2 gene in Xenopus laevis

The cloning and sequencing of complementary DNAs corresponding to the two copies (a and b) of the Xenopus laevis gene for hnRNP E2 is presented. Comparison of the two sequences reveals that while they are somewhat divergent at the nucleotide level, they are very conserved at the amino acid level. The analysis also showed two transcripts of different length (alpha and beta), likely generated by alternative processing. There are indications that either gene copy can generate both type of transcripts. Northern blot analysis in oocytes and developing embryos showed that hnRNP E2 RNA is constantly present and that increases in amount at tadpole stage. A semiquantitative reverse transcriptase polymerase chain reaction analysis performed with RNA from developing embryos showed that long (alpha) transcript accumulation is constant during development, whereas the short one (beta) accumulation increases at later stages, thus determining the observed increase in total RNA. Nucleo-cytoplasm localization experiments indicated that in oocyte hnRNP E2 is exclusively cytoplasmic, whereas in somatic cells it is distributed in both compartments. Comparison of the amino acid sequence of the two X. laevis hnRNP E2 with the corresponding mammalian sequences shows a high homology along the molecule except for the region subjected to alternative splicing, which is completely different. Moreover, there are indications that the homologous of mammalian hnRNP E1 gene, very related to and derived from hnRNP E2 by retrotransposition, is not expressed or even not present in X. laevis, suggesting that mammalian hnRNP E1 gene may have originated after mammal/amphybia divergence.

Translational control of ribosomal protein L4 mRNA is required for rapid neurite regeneration

Under some circumstances neurons can be primed to rapidly regenerate injured neuritic processes independent of new gene expression. Such transcription-independent neurite extension occurs in adult rat sensory neurons cultured after sciatic nerve crush and in NGF-differentiated PC12 cells whose neurites have been mechanically sheared. In the PC12 cells, neurite regeneration occurs by means of translational control of mRNAs which were transcribed prior to neurite injury. The survival of such translationally regulated mRNAs is relatively short in the differentiated PC12 cells (< or =10 h). By subtractive hybridization, we have isolated a short-lived mRNA from differentiated PC12 cells. This mRNA, which encodes the ribosomal protein L4, is translationally regulated during neurite regeneration in PC12 cells. Antisense oligonucleotides to L4 mRNA inhibit neurite regeneration from the differentiated PC12 cells as well as axonal elongation from conditioned sensory neurons, indicating that ongoing translation of L4 mRNA is needed for these forms of rapid transcription-independent neurite growth. Taken together, these data point to the importance of translational regulation of existing neuronal mRNAs in the regenerative responses to neuronal injury. Although there are other examples of neuronal translational control, there are no other known neuronal proteins whose levels are regulated predominantly by translational rather than transcriptional control.

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

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

Regulation of early expression of Dlx3, a Xenopus anti-neural factor, by beta-catenin signaling

The ectoderm of the pre-gastrula Xenopus embryo has previously been shown to be at least partially patterned along the dorsal-ventral axis. The early expression of the anti-neural homeodomain gene Dlx3 is localized to the ventral ectoderm by a mechanism that occurs prior to gastrulation and is independent of the Spemann organizer. The repression of Dlx3 is mediated by signaling though beta-catenin, but is probably not dependent on the induction of the Xnr3 or chordin genes by beta-catenin. We propose a model in which this early regulation of Dlx3 accounts for the pro-neural bias of dorsal ectoderm.

cDNA cloning and developmental expression of cellular nucleic acid-binding protein (CNBP) gene in Xenopus laevis

The cloning and sequencing of a cDNA corresponding to one of the two Xenopus cellular nucleic acid binding protein (CNBP) genes are presented. Comparison of this cDNA sequence (xCNBP2) with the other previously reported (xCNBP1) reveals that, while the cDNA sequences are somewhat divergent, the amino acid sequences are mostly unchanged. It has been determined that both gene copies can generate a shorter transcript, likely due to alternative splicing, as previously demonstrated in human cells. The comparison of the cDNA sequences of Xenopus and of other species shows that the missing cDNA tract of Xenopus does not coincide with the others, consistent with the utilization of different splicing donor sites. The two gene copies are expressed at comparable levels, since the two corresponding mRNAs are similarly represented both in oocyte and embryo poly(A)(+) RNA. However, the shorter CNBP transcripts are slightly less represented than the longer CNBP transcripts, in both the oocyte and embryo. CNBP mRNA accumulation during development decreases before the mid-blastula stage and increases again thereafter. The polysome association of CNBP mRNA and the binding activity of CNBP to its target sequence of ribosomal protein mRNA 5'UTR have been analysed during development.

Isolation, characterization and expression of the Xenopus laevis ribosomal protein S6 gene

We report the isolation and characterization of genomic DNA clones encoding Xenopus ribosomal protein (rp) S6. A human rpS6 cDNA was used to screen a genomic DNA library, and this led to the isolation of a genomic clone encompassing the complete rpS6 gene locus. DNA sequencing and primer extension analysis indicate that Xenopus rpS6 is structurally analogous to the mammalian rpS6 genes, and its transcription starts at two sites within the same polypyrimidine tract of 10 bases. A series of deletions of the 5' region of the Xenopus rpS6 gene were fused to the chloramphenicol acetyltransferasereporter gene and transfected into COS-1 cells. The results suggest that the regulatory regions of the Xenopus rpS6 gene are clearly distinct from those earlier reported for the human rpS6 gene. Northern blot analysis of stage-specific embryonic RNA demonstrated an uniform rpS6 transcription during embryogenesis. Southern blot and PCR analyses indicate that the Xenopus rpS6 gene is pseudotetraploid in the Xenopus genome.

Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes

We have identified gas5 (growth arrest-specific transcript 5) as a non-protein-coding multiple small nucleolar RNA (snoRNA) host gene similar to UHG (U22 host gene). Encoded within the 11 introns of the mouse gas5 gene are nine (10 in human) box C/D snoRNAs predicted to function in the 2'-O-methylation of rRNA. The only regions of conservation between mouse and human gas5 genes are their snoRNAs and 5'-end sequences. Mapping the 5' end of the mouse gas5 transcript demonstrates that it possesses an oligopyrimidine tract characteristic of the 5'-terminal oligopyrimidine (5'TOP) class of genes. Arrest of cell growth or inhibition of translation by cycloheximide, pactamycin, or rapamycin-which specifically inhibits the translation of 5'TOP mRNAs-results in accumulation of the gas5 spliced RNA. Classification of gas5 as a 5'TOP gene provides an explanation for why it is a growth arrest specific transcript: while the spliced gas5 RNA is normally associated with ribosomes and rapidly degraded, during arrested cell growth it accumulates in mRNP particles, as has been reported for other 5'TOP messages. Strikingly, inspection of the 5'-end sequences of currently known snoRNA host gene transcripts reveals that they all exhibit features of the 5'TOP gene family.

Differential expression of Xenopus ribosomal protein gene XlrpS1c

Components of the translational machinery of the cell, including ribosomal proteins, are generally considered to be clear examples of housekeeping genes with a spatially ubiquitous distribution of messenger RNA during embryonic development. Here we present data based upon in situ hybridization experiments as well as RNase protection assays, demonstrating that Xenopus ribosomal protein gene S1 is differentially expressed in a complex and spatially distinct pattern during embryogenesis. We observed dramatically high levels of expression in some tissues, such as the branchial arches, otic vesicles, optic vesicles and somites and virtually no expression in other tissues, such as the cement gland, epidermis and notochord. Moreover, ribosomal protein genes S22, L1, and L5 display expression patterns nearly identical to S1. Our data is consistent with a model of ribosomal gene expression according to which ribosomal protein genes (or perhaps a subset of ribosomal protein genes) may be expressed at low levels in all tissues, but are abundantly expressed in other cell types reflecting a dynamic and complex pattern of transcriptional control throughout embryonic development.

Antagonistic actions of activin A and BMP-2/4 control dorsal lip-specific activation of the early response gene XFD-1' in Xenopus laevis embryos

Transcription of the early response gene XFD-1' (XFKH1) in the dorsal lip (Spemann organizer) of Xenopus embryos is activated by dorsal mesoderm inducing factors. Promoter studies revealed the presence of an activin A response element (ARE) which is both necessary and sufficient for transcriptional activation of reporter genes in animal cap explants incubated with activin A. Surprisingly, this ARE is also active within vegetal explants in the absence of exogenously added inducers, but an additional inhibitory response element prevents transcription of the XFD-1' gene in the ventral/vegetal region of the embryo in vivo. This element is located upstream of the ARE, it responds to bone morphogenic proteins 2 and 4 (BMP-2/4) triggered signals and it overrides the activating properties of the ARE. Expression patterns of BMP-2 and BMP-4 in the late blastula stage embryo and, especially, their absence from the dorsal blastopore lip may thus control the spatial transcription of the XFD-1' gene. Accordingly, the temporal activation and the spatial restriction of XFD-1' gene activity to the Spemann organizer is regulated by antagonistic actions of two distinct members of the TGF-beta family (activin and BMP) which act on different promoter elements.

A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site

The mechanism by which intron-containing RNAs are recognized by the splicing machinery is only partly understood. A nuclear cap-binding complex (CBC), which specifically recognizes the monomethyl guanosine cap structure carried by RNA polymerase II transcripts, has previously been shown to play a role in pre-mRNA splicing. Using a combination of splicing complex and psoralen cross-linking analysis we demonstrate that CBC is required for efficient recognition of the 5' splice site by U1 snRNP during formation of E (early) complex on a pre-mRNA containing a single intron. However, in a pre-mRNA containing two introns, CBC is not required for splicing of the cap distal intron. In this case, the presence of an intact polypyrimidine tract in the cap-proximal intron renders splicing of the cap-distal intron independent of CBC. These results support models in which the splice sites in a pre-mRNA are originally recognized by interactions spanning exons. The defects in splicing and U1 snRNP binding caused by CBC depletion can be specifically reversed by recombinant CBC. In summary, efficient recognition of the cap-proximal 5' splice site by U1 snRNP is facilitated by CBC in what may be one of the earliest steps in pre-mRNA recognition. Data in Colot et al. (this issue) indicate that this function of CBC is conserved in humans and yeast.

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

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

Structure and expression of ribosomal protein genes in Xenopus laevis

In Xenopus laevis, as well as in other vertebrates, ribosomal proteins (r-proteins) are coded by a class of genes that share some organizational and structural features. One of these, also common to genes coding for other proteins involved in the translation apparatus synthesis and function, is the presence within their introns of sequences coding for small nucleolar RNAs. Another feature is the presence of common structures, mainly in the regions surrounding the 5' ends, involved in their coregulated expression. This is attained at various regulatory levels: transcriptional, posttranscriptional, and translational. Particular attention is given here to regulation at the translational level, which has been studied during Xenopus oogenesis and embryogenesis and also during nutritional changes of Xenopus cultured cells. This regulation, which responds to the cellular need for new ribosomes, operates by changing the fraction of rp-mRNA (ribosomal protein mRNA) engaged on polysomes. A typical 5' untranslated region characterizing all vertebrate rp-mRNAs analyzed to date is responsible for this translational behaviour: it is always short and starts with an 8-12 nucleotide polypyrimidine tract. This region binds in vitro some proteins that can represent putative trans-acting factors for this translational regulation.

Self-cleaving motifs are found in close proximity to the sites utilized for U16 snoRNA processing

A class of small nucleolar RNAs (snoRNAs) is encoded in introns of protein-coding genes. The U16 snoRNA belongs to this class; it is encoded in the third intron of the Xenopus laevis (Xl) L1 ribosomal protein encoding gene and is released from the pre-mRNA by processing both in vivo and in vitro systems. In this paper, we show that in close proximity to the U16 snoRNA processing sites, sequences displaying self-cleaving activity are present. These elements are conserved in the two copies of the Xl L1 and in the single copy of the X. tropicalis L1. The catalytic activity corresponds to that already described for the minimal hairpin ribozyme [Dange et al., Science 242 (1990) 585-588]; it is Mn(2+)-dependent, produces 2'-3' cyclic phosphate and 5'-OH termini and comprises an essential GAAA element. Here we show that the 2'-OH group of the G residue is essential for catalysis.

Sequence of the cDNA and gene coding for ribosomal protein S1 of Xenopus laevis

The cloning and complete sequencing of one of the two gene copies coding for ribosomal protein (r-protein) S1 in Xenopus laevis and of the corresponding cDNA are reported. The comparison of the sequence of this cDNA (S1b) with the other (S1a) previously reported, reveals that, while the two DNA sequences have diverged somewhat, the amino-acid sequences are mostly unchanged. The two gene copies are apparently expressed at comparable levels, since the two corresponding mRNAs are similary represented in oocyte poly(A) RNA. The S1b gene has a total length of about 12000 nt and is composed of seven exons and six introns. By primer extension, it has been determined that the transcription start point is located in a pyrimidine-rich tract, as observed for all r-protein genes of X. laevis and other vertebrates so far analyzed. A computer analysis of the S1 sequence has shown the presence of a 150-nt sequence repeated in introns 3, 5 and 6, which is homologous to the one reported in the first intron of mammalian r-protein S3 gene. Furthermore, a 130-nt sequence is tandemly repeated 2.5 times at each of the two sites near the beginning and near the end of the first intron.

Aspects of regulation of ribosomal protein synthesis in Xenopus laevis. Review

The work carried out in the authors' laboratories on the structure and expression of ribosomal protein genes in Xenopus is reviewed, with some comparisons with other systems. These genes form a class that shares several structural features, especially in the region surrounding the 5' ends. These similar structures appear to be involved in coregulated expression that is attained at various regulatory levels: transcriptional, transcript processing and stability, and translational. Particular attention is paid here to the one operating at the translational level, which has been studied during Xenopus oogenesis and embryogenesis, and also during nutritional changes of Xenopus cultured cells. This regulation, which responds to the cellular need for new ribosomes, operates by changing the fraction of rp-mRNA engaged on polysomes, leaving each translated rp-mRNA molecule always fully loaded with ribosomes. Responsible for this translational behaviour is the typical 5'UTR, which characterizes all rp-mRNAs analyzed up to now, and that can bind in vitro some proteins, putative trans-acting factors for this translational regulation.

Human ribosomal protein L4: cloning and sequencing of the cDNA and primary structure of the protein

The cloning and sequencing of a cDNA for human ribosomal protein L4 is reported. The corresponding mRNA has a very short 5' untranslated region initiating with a sequence of 12 pyrimidines, characteristic of all vertebrate ribosomal protein mRNAs. The deduced amino acid sequence shows that human ribosomal protein L4 has 425 amino acid residues and a calculated molecular mass of 47,821 Da. Comparison with the homologous counterparts of Xenopus, Drosophila and yeast shows that this protein has a very conserved amino-terminus region and an extremely divergent carboxyl-terminus portion.

Sequence of the gene coding for ribosomal protein S8 of Xenopus laevis

We present here the cloning and the entire sequence of one of the two gene copies coding for ribosomal protein (r-protein) S8 in Xenopus laevis (corresponding to r-protein S7 in rat) and its flanking regions. The S8a gene contains seven exons and six introns for a total length of about 12,700 bp coding for a mRNA of 663 nucleotides (nt) plus a poly(A) tail. Mapping of the 5' end of the gene has shown that the transcription start point is located in a pyrimidine-rich tract, as has been observed for all r-protein-encoding genes of X. laevis and other vertebrates so far characterized. A computer analysis of the S8a sequence has revealed the presence of a 220-nt sequence repeated, with some variations, once in each of the six introns. RNA analysis by hybridization with oligo probes specific for the two gene copies coding for r-protein S8 has demonstrated that the two of them are expressed at similar levels both in oocytes and in embryos.

The pyrimidine sequence encompassing the transcription start point of Xenopus laevis ribosomal-protein-encoding genes is not obligatory for activity in oocytes

The genes coding for ribosomal proteins (r-proteins) in Xenopus laevis have a stretch of about 20 pyrimidines (Y) at their 5' end, in the middle of which is localized the main transcription start point (tsp). To obtain information about its possible functional significance, we have introduced by site-directed mutagenesis one or more purines at various positions within the oligo(Y) tract present at the 5' end of the gene coding for r-protein S19 of X. laevis. The effect of these mutations on transcription and translation of a reporter-coding sequence has been evaluated by DNA microinjection in X. laevis oocytes. We show that an uninterrupted stretch of pyrimidines is not necessary for efficient transcription and translation of the reporter gene in the X. laevis oocyte. This finding does not exclude the possibility that this sequence is involved in transcription and/or translation regulation in some developmental situations different from oogenesis.

Individual variability in the translational regulation of ribosomal protein synthesis in Xenopus laevis

Ribosomal protein synthesis is regulated by controlling the fraction of mRNA associated with polysomes. It is known that this value changes in different developmental stages during Xenopus embryogenesis or, more generally, with changing cell growth conditions. We present here an analysis of the proportion of mRNA loaded on polysomes, carried out with probes for five different ribosomal proteins on several batches of Xenopus embryos obtained from different individuals. The results obtained indicate the existence of probe-dependent and individual differences, which reflect genetic variations in the cis- and trans-acting regulatory elements responsible for translational regulation. The fraction of ribosomal protein mRNA loaded onto polysomes can be used as an index of an individual's capacity for ribosome production.

Inefficient in vitro splicing of the regulatory intron of the L1 ribosomal protein gene of X.laevis depends on suboptimal splice site sequences

The splicing of the third intron of the L1 r-protein gene of X.laevis was studied in the heterologous in vitro HeLa nuclear system. Despite the evolutionary distance, the cis-elements responsible for the default process play a similar role in the two organisms. Analysis of the splicing of various mutant substrates showed that the 5' splice site is primarily responsible for the low efficiency of splicing of the third intron. The suboptimal 5' splice site sequence leads to the utilization of an upstream alternative site which corresponds to the one utilized in vivo. The accumulation of splicing intermediates in the in vitro system allowed the identification of the branch site and of the branch consensus sequence. In contrast, the in vivo regulatory mechanism involving cleavage of the pre-mRNA is not mimicked in the HeLa extract.

Equipotent mouse ribosomal protein promoters have a similar architecture that includes internal sequence elements

The promoters of the mouse ribosomal protein genes rpL30, rpL32, and rpS16 are of equal strength, as indicated by in vivo measurements of polymerase loading and by their relative efficiency in driving the expression of a linked reporter gene. The equipotency of these promoters appears to derive from a remarkably similar architecture in which five or more elements are distributed over a 200-bp region that spans a polypyrimidine-embedded cap site. Three trans-acting factors are shared by the rpL30 and rpL32 promoters, one of which, delta, recognizes a common CNGCCATCT motif in the first (untranslated) exons. Site-specific mutagenesis demonstrated that delta-factor binding is critical for rpL30 promoter function. The repeated occurrence of this novel promoter architecture among ribosomal protein genes with very different coding specificities is most readily explained by convergent evolution.

The primary structure of rat ribosomal protein L37a

The amino acid sequence of rat ribosomal protein L37a was deduced from the sequence of nucleotides in recombinant cDNAs isolated in Yamagata and in Chicago and confirmed from the NH2-terminal amino acid sequence of the protein. Ribosomal protein L37a contains 91 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular mass of 10143 Da.

The primary structure of rat ribosomal protein L21

The covalent structure of rat ribosomal protein L21 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2-terminal amino acid sequence of the protein. Ribosomal protein L21 contains 159 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 18,322. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 16-23 copies of the L21 gene. The mRNA for the protein is about 680 nucleotides in length.

The primary structure of rat ribosomal protein S4

The amino acid sequence of the rat 40 S ribosomal subunit protein S4 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2-terminal amino-acid sequence of the protein. Ribosomal protein S4 has 282 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 31,841. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 7-11 copies of the S4 gene. The mRNA for the protein is about 1 kb in length. Rat S4 is homologous to Saccharomyces cerevisiae YS6. The protein contains a possible internal duplication of 11 residues.

The primary structure of rat ribosomal protein S10

The amino acid sequence of rat ribosomal protein S10 was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the NH2-terminal amino acid sequence of the protein. Ribosomal protein S10 contains 165 amino acids and has a molecular mass of 18917 Da. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 17-20 copies of the S10 gene. The mRNA for the protein is about 750 nucleotides in length. Ribosomal protein S10 has several possible internal duplications; one is a tandem repeat of ten residues that is basic and contains two or three prolines.

Expression of ribosomal protein genes and regulation of ribosome biosynthesis in Xenopus development

Studies on ribosome biosynthesis in developing Xenopus oocytes and embryos, and after microinjection of cloned ribosomal-protein genes, have revealed that the synthesis of ribosomal proteins (r-proteins) is controlled by two types of regulation: (1) a post-transcriptional regulation, operated by feedback of the r-proteins themselves, controls processing and stability of r-protein transcripts and thus the amount of the corresponding mRNA present in the cell; and (2) a translational regulation controls the efficiency of utilization of r-protein mRNA (rp-mRNA) in response to the cellular needs for new ribosomes.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

Identification of an orthologous mammalian cytokeratin gene. High degree of intron sequence conservation during evolution of human cytokeratin 10

Among the human acidic (type I) cytokeratins, components 10 and 11 are especially interesting, as they are under various kinds of expression control. They are synthesized in the suprabasal cell layers of certain stratified epithelia, notably epidermis, in an endogenous differentiation program; they are expressed in certain epithelial tumours but not in others; they can appear de novo in certain pathological situations such as in squamous metaplasias; and their expression in vivo and in vitro is under positive influence of extracellular calcium concentrations and is reduced in the presence of vitamin A or other retinoids. To provide a basis for studies of the various regulatory elements, we have isolated the human gene encoding cytokeratin 10, using a cDNA probe derived from the corresponding bovine gene, and have sequenced the mRNA coding region as well as adjacent regions approximately 1500 bases 5' upstream and 1000 bases 3' downstream. The eight exons encode a polypeptide 59,535 Mr, i.e. somewhat larger than the corresponding bovine and murine proteins. The deduced amino acid sequences display a high degree of homology, which is not restricted to the exons and the 5' and 3' adjacent regions but, surprisingly, is also evident in the seven introns, some of which contain extended sequence elements with 70% identical nucleotides and more, i.e. similar to the homology in the adjacent exons. This exceptionally high level of conservation of intron sequences is discussed in relation to the recently accumulating evidence of the occurrence of intron sequences important in the regulation of the expression of members of other multigene families during development.

Isolation and nucleotide sequences of cDNAs for Xenopus laevis ribosomal protein S8: similarities in the 5' and 3' untranslated regions of mRNAs for various r-proteins

Recombinant clones specific for ribosomal protein (r-protein) S8 have been isolated from a Xenopus laevis cDNA bank. Sequence analysis shows that they are of two types, derived from two different gene copies originating from gene duplication. The two cDNAs differ in several silent sites and code for the same S8 protein whose complete amino acid sequence has been derived. Sequence comparison of S8 mRNAs with those for other X. laevis r-proteins, has revealed interesting similarities in the 5' and 3' untranslated regions. These could be involved in r-protein synthesis regulation which we have previously shown to occur mainly at post-transcriptional and translational levels.

Structural basis for autogenous regulation of Xenopus laevis ribosomal protein L1 synthesis at the splicing level

It is known that the injection of the Xenopus laevis ribosomal protein L1 gene into oocytes causes the accumulation of immature L1 transcripts due to a specific block of splicing of the second and third introns. In this paper the secondary structures of these introns in pre-mRNA have been constructed. It has been shown that they share homology with 28 S rRNA. The putative RNA-binding segment of L1 has also been predicted. These results are interpreted as the structural basis for autogenous regulation of X. laevis ribosomal protein L1 synthesis at the splicing level.

Translational inactivation of ribosomal protein mRNAs during Xenopus oocyte maturation

Ribosomal protein synthesis ceases upon maturation of Xenopus oocytes. We find that this cessation results from the dissociation of ribosomal protein mRNAs from polysomes and is accompanied by the deadenylation of these transcripts. A synthetic mRNA encoding ribosomal protein L1, microinjected into stage VI oocytes, is deadenylated and released from polysomes upon maturation. Our results indicate that sequences located within 387 bp of the 3' terminus of L1 mRNA direct both the deadenylation and polysomal release of this ribosomal protein mRNA. The proper translational regulation of an exogenous ribosomal protein mRNA in microinjected oocytes provides a basis for determining the sequence specificity for the differential utilization of maternal mRNAs during oocyte maturation.

Structure of the mouse nucleolin gene. The complete sequence reveals that each RNA binding domain is encoded by two independent exons

Nucleolin is a multifunctional nucleolar protein involved in the synthesis, packaging and maturation of pre-rRNA in eukaryotic cells. We describe the molecular organization and complete sequence of the mouse nucleolin gene, the first higher eukaryotic gene encoding a protein that is both an RNA binding protein involved in rRNA processing and a specific nucleolar protein. The nucleolin gene extends over 9000 base-pairs and is split into 14 exons that encode the 706 amino acid residues of the protein. The promoter sequence is G + C-rich (67% G + C) with four G/C boxes, it lacks bona fide TATA and CAAT boxes and shows capping site heterogeneity. The existence of pyrimidine-rich motifs, similar to those found in the promoter of ribosomal protein genes, could be relevant to the co-regulation of genes whose products are involved in ribosome biogenesis. Nucleolin contains four RNA binding domains, each about 80 amino acid residues long, which include the 11-residue core ribonucleoprotein consensus motif. Each domain is encoded by two exons, with an intervening sequence interrupting the conserved core motif at roughly the same amino acid position. This latter result suggests that the RNA binding domains are composed of two independent subdomains, whose functions remain to be determined.

Post-translational control of ribosomal protein L1 accumulation in Xenopus oocytes

A functional ribosomal protein mRNA, encoding the 60 S subunit protein L1, has been synthesized in vitro using bacteriophage SP6 RNA polymerase. This mRNA directs the synthesis of a product indistinguishable from L1 protein purified from Xenopus ovarian ribosomes. Our results show that L1 synthesis in stage VI oocytes increases in response to microinjection of exogenous SP6-L1 mRNA, but excess L1 protein is not stably accumulated. These results indicate that dosage compensation does not occur at the translational level for this ribosomal protein mRNA and that the abundance of this protein in fully grown oocytes is subject to post-translational regulation.

Depletion of Saccharomyces cerevisiae ribosomal protein L16 causes a decrease in 60S ribosomal subunits and formation of half-mer polyribosomes

We constructed yeast strains containing deletion-insertion null alleles of the RPL16A or RPL16B genes encoding the 60S ribosomal subunit protein L16 to determine the role of L16 in the synthesis and function of ribosomes. Strains lacking a functional RPL16A gene grow as rapidly as wild type, whereas those containing a null allele of RPL16B grow more slowly than wild type. RNA analysis using RPL16 probes revealed that both RPL16 genes are transcribed and that RPL16B transcripts accumulate to twice the level of RPL16A transcripts. No evidence was obtained for the occurrence of dosage compensation at the level of RPL16 mRNA accumulation in either mutant. Strains lacking both RPL16 genes are apparently inviable, demonstrating that L16 is an essential yeast ribosomal protein. Introduction of an extra copy of either RPL16 gene into rpl16b mutants restored wild-type growth rates, indicating that the two forms of the L16 protein are interchangeable. rpl16 mutants are deficient in 60S ribosomal subunits relative to 40S subunits. 43S preinitiation complexes accumulate in half-mer polyribosomes in the absence of sufficient 60S subunits. We postulate that the slow-growth phenotype of rpl16 mutants results from the perturbation of initiation of protein synthesis.

Expression of the gene for ribosomal protein L1 in Xenopus embryos: alteration of gene dosage by microinjection

Cloned gene for Xenopus ribosomal protein L1 was injected into fertilized eggs, and its expression was analyzed during the period of embryo development when the mRNAs produced by the endogenous ribosomal protein genes are still silent due to a translational control. The injected genes replicated extensively, and a 10-fold excess of L1 mature transcript accumulated in the embryo. This was accompanied by a small amount of incompletely processed L1 RNA that still contained one out of nine introns, a molecule never observed in normal conditions. The excess mature L1 mRNA was distributed between polysomes and messenger ribonucleoproteins (mRNPs) in the same relative proportion observed in control embryos of the same stage. Therefore, more L1 mRNA was loaded onto polysomes and caused the appearance of L1 protein when this was not yet detectable in control embryos. The results suggest a relationship between the excess amount of L1 protein and the alteration in processing of its transcripts.

Expression of ribosomal protein genes during Xenopus development

The Xenopus ribosomal protein genes provide an excellent system to elucidate the complex regulation encompassing 60 functionally related proteins present in equimolar amounts in ribosomal subunits. Oogenesis and embryogenesis provide unique opportunities to investigate ribosome biosynthesis in situations wherein gene activation of individual components is uncoupled from assembly of the ribosomal subunits. This chapter has focused on the basic parameters that control ribosomal protein gene expression during development. Translational control is clearly a major level for coordinating the regulation of these genes during development, as is posttranslational stability of the ribosomal proteins and RNA splicing of the L1 gene. In addition to these levels of control under active investigation, a number of intriguing problems remain to be addressed in any detail. For example, the mechanisms that balance ribosomal protein production with subunit assembly in oocytes remain to be determined. Resolution of these events must also define the processes by which ribosomal proteins, upon synthesis in the cytoplasm, are first translocated to the nucleus and subsequently to the nucleolus for subunit assembly. Functional approaches in which these genes are assayed for accurate developmental control in microinjected oocytes and fertilized eggs will undoubtedly provide information on the synthesis of this eukaryotic organelle and the signals responsible for altering these processes at different developmental stages.

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.

Intervening sequences exhibit distinct vocabulary

Little is known about the origin and function of eukaryotic introns. Application of a novel linguistic approach to the analysis of intervening sequences reveals, however, that they exhibit a specific non-random vocabulary whose major feature is the utilization of mirror-symmetrical words ("mirrorrim"). Introns also manifest a significant tendency to avoid local complementarities. Possible biological implications of the corresponding loop regions in the RNA transcripts are discussed.

Complementarity of conserved sequence elements present in 28S ribosomal RNA and in ribosomal protein genes of Xenopus laevis and Xenopus tropicalis

The sequence analysis of the L1 ribosomal protein (r-protein) gene of Xenopus laevis has revealed a strong homology in four out of the nine introns of the gene; this homology region spans 60 nucleotides (nt) with 80% homology [Loreni et al., EMBO J. 4 (1985) 3483-3488]. We have extended our analysis to X. tropicalis, a species which is closely related to X. laevis. Partial sequencing of the isolated L1 gene has revealed that these 60-nt homology regions are also present in at least two introns of the X. tropicalis L1 gene. Computer analysis has revealed that perfect nt sequence complementarity exists between 13 nt of this intron region and the 28S ribosomal RNA in a region which is conserved in all eukaryotes, suggesting a possible base-pairing interaction between these two sequences.