A leucine zipper-like motif and a basic region-leucine zipper-like element in rat ribosomal protein L13a. Identification of the tum- transplantation antigen P198

Ribosomal versus non-ribosomal cellular antigens: factors determining efficiency of indirect presentation to CD4+ T cells

Proteins released from dying cells can be taken up and presented by antigen-presenting cells (APC) to T cells. While the presentation of such self antigens may lead to beneficial anti-tumour responses, in autoimmune disease it leads to pathological immune responses. The sub-set of self proteins targeted in autoimmune disease is circumscribed, and certain cellular components such as ribonucleoprotein (RNP) complexes are often targeted. Although explanations for this antigen selectivity have been proposed, there has been little direct testing of these hypotheses. We and others previously showed that ribosomal proteins, targeted in autoimmune disease, are also targets of anti-tumour T-cell responses. We asked whether particular properties of ribosomal proteins such as incorporation into RNP complexes or sub-cellular localization enhance ribosomal protein presentation by APC to CD4(+) T cells. Ribosomal protein antigens within purified intact ribosomes or free of the ribosomes were equally well taken up and presented by APC, demonstrating that inclusion of ribosomal proteins into an RNP complex does not confer an advantage. However, antigens localized to ribosomes within apoptotic cells were less efficiently taken up and presented by APC than the same antigens localized diffusely throughout the cell. This suggests that presentation of ribosomal proteins is somehow down-regulated, possibly to facilitate presentation of other less-abundant intracellular proteins. Consequently, the explanation for the frequent targeting of ribosomal proteins by both autoimmune and anti-tumour T-cell responses is not at the level of uptake from apoptotic cells and must be sought elsewhere.

Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition

Calmodulin (CaM) signaling involves important, wide spread eukaryotic protein-protein interactions. The solved structures of CaM associated with several of its binding targets, the distinctive binding mechanism of CaM, and the significant trypsin sensitivity of the binding targets combine to indicate that the process of association likely involves coupled binding and folding for both CaM and its binding targets. Here, we use bioinformatics approaches to test the hypothesis that CaM-binding targets are intrinsically disordered. We developed a predictor of CaM-binding regions and estimated its performance. Per residue accuracy of this predictor reached 81%, which, in combination with a high recall/precision balance at the binding region level, suggests high predictability of CaM-binding partners. An analysis of putative CaM-binding proteins in yeast and human strongly indicates that their molecular functions are related to those of intrinsically disordered proteins. These findings add to the growing list of examples in which intrinsically disordered protein regions are indicated to provide the basis for cell signaling and regulation.

Insertional inactivation of the L13a ribosomal protein gene of Drosophila melanogaster identifies a new Minute locus

We have utilized a transposable P element construct to scan the genome for modifiers of Drosophila Notch pathway phenotypes. From a collection of 2000 inserts we obtained two enhancers and one suppressor. Sequence analysis of the insertion regions demonstrated that two modifiers affect known components of the Notch pathway, whereas the third is an insert in the gene encoding ribosomal protein L13a at cytogenetic region 83B6-7. The insert in the RpL13A coding region creates a classic Minute mutation which enhances Notch pathway wing phenotypes. This report adds RpL13A to the list of Drosophila ribosomal protein genes that cause Minute phenotypes when mutated.

Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control

Transcript-specific translational control is generally directed by binding of trans-acting proteins to structural elements in the untranslated region (UTR) of the target mRNA. Here, we elucidate a translational silencing mechanism involving regulated release of an integral ribosomal protein and subsequent binding to its target mRNA. Human ribosomal protein L13a was identified as a candidate interferon-Gamma-Activated Inhibitor of Translation (GAIT) of ceruloplasmin (Cp) mRNA by a genetic screen for Cp 3'-UTR binding proteins. In vitro activity of L13a was shown by inhibition of target mRNA translation by recombinant protein. In response to interferon-gamma in vivo, the entire cellular pool of L13a was phosphorylated and released from the 60S ribosomal subunit. Released L13a specifically bound the 3'-UTR GAIT element of Cp mRNA and silenced translation. We propose a model in which the ribosome functions not only as a protein synthesis machine, but also as a depot for regulatory proteins that modulate translation.

Isolation of the melanoma-associated antigen p23 using antibody phage display

The general responsiveness of human melanoma to immunotherapy has been well established, but active immunotherapy of melanoma has been hampered by insufficient information on the immunogenicity of melanoma-associated Ags in patients. In this study, we isolated a recombinant phage-Fab clone (A10-5) from a phage-Fab library derived from the B cells of a melanoma patient in remission after immunotherapy. Purified A10-5 Fab bound at high levels to cultured melanoma cell lines and to tissue sections of metastatic and vertical growth phase primary melanoma, but not to radial growth phase primary melanoma, nevi, or normal skin. A10-5 Fab bound to both the surface and the cytoplasm of cultured melanoma cells, but only to the cytoplasm of cultured fibroblasts. Western blot analysis revealed A10-5 Fab reactivity with a 33- and a 23-kDa glycoprotein under nonreducing conditions, and with a 23-kDa protein only under reducing conditions. A cDNA with an open reading frame predicted to encode a 23-kDa protein was cloned by screening a melanoma cell cDNA library with A10-5 Fab. This protein (p23) is the human homologue of the murine tumor transplantation Ag P198 that interacts with the cytoplasmic domain of ErbB-3 expressed by melanoma cells. Thus, the Ab phage display method has identified a novel, stage-specific melanoma-associated Ag that may have therapeutic and diagnostic value.

The rpl16a gene for ribosomal protein L16A identified from expressed sequence tags is differentially expressed during sexual development of Aspergillus nidulans

We obtained 305 expressed sequence tags (ESTs), which are from the poly(A) site to the most proximal MboI site, from mycelia at the early sexual developmental (ESD) stage of Aspergillus nidulans. By comparison of these ESTs with those obtained previously from the vegetative stage and from the late sexual developmental stage followed by Northern blot analyses, genes of 17 ESTs were identified as being expressed more abundantly at the ESD stage than at the vegetative stage. Five of 17 genes were expressed more abundantly in the presence of the veA gene or the nsdD gene, suggesting that these 5 genes may be involved in sexual development. In a gene of one EST, appearing three times among 305 ESTs and identified by GenBank, polyadenylation seemed to occur at two sites. Nucleotide sequences of the gene having the EST and its cDNA revealed that the gene can code for a 202-amino-acid polypeptide with an estimated molecular mass of 23 kDa. The deduced amino acid showed 73% identity to Saccharomyces cerevisiae ribosomal protein L16A (RPL16A), and therefore the gene was named rpl16a. A. nidulans RPL16A had a putative leucine zipper motif and a basic leucine zipper motif like those of other organisms. The expression level of the rpl16a gene, present as a single copy in this organism, reached a maximum after 2 h, decreased thereafter, and increased again 30 to 50 h after the end of induction of sexual development. These results clearly indicated that the rpl16a gene is expressed differentially during sexual development.

Ribosomal proteins in cell proliferation and apoptosis

Ribosomal proteins have the complex task of coordinating protein biosynthesis to maintain cell homeostasis and survival. Recent evidence suggests that a number of ribosomal proteins have secondary functions independent of their involvement in protein biosynthesis. A number of these proteins function as cell proliferation regulators and in some instances as inducers of cell death. Specifically, expression of human ribosomal protein L13a has been shown to induce apoptosis, presumably by arresting cell growth in the G2/M phase of the cell cycle. In addition, inhibition of expression of L13a induces apoptosis in target cells, suggesting that this protein is necessary for cell survival. Similar results have been obtained in the yeast Saccharomyces cerevisiae, where inactivation of the yeast homologues of L13a, rp22 and rp23, by homologous recombination results in severe growth retardation and death. In addition, a closely related ribosomal protein, L7, arrests cells in G1 and also induces apoptosis. Thus, it appears that a group of ribosomal proteins may function as cell cycle checkpoints and compose a new family of cell proliferation regulators.

The ribosomal protein L34 gene from the mosquito, Aedes albopictus: exon-intron organization, copy number, and potential regulatory elements

We describe the structural analysis of genomic DNA encoding ribosomal protein (rp) L34 from the mosquito, Aedes albopictus. Comparison of genomic DNA sequences encompassing approximately 8 kb with the rpL34 cDNA sequence showed that the gene contains three exons and two introns, encoding a primary transcript with a deduced size of 6196 nucleotides from the transcription start site to the polyadenylation site. Exon 1, which is not translated, measures only 45 bp, and is separated from Exon 2 by a 359 bp intron. Exon 2 measures 78 bp, and contains the AUG translation initiation codon 14 nucleotides downstream of its 5'-end. Downstream of Exon 2 is a 5270 bp intron, followed by the remainder of the coding sequence in Exon 3, which measures 444 bp including the polyadenylation signal. We used a novel PCR-based procedure to obtain 1.7 kb of DNA upstream of the rpL34 gene. Like the previously described Ae. albopictus rpL8 gene and various mammalian rp genes, the DNA immediately upstream of the rpL34 gene lacks the TATA box, and the rpL34 transcription initiation site is embedded in a characteristic polypyrimidine tract. The 5'-flanking DNA contained a number of cis-acting elements that potentially interact with transcription factors characterized by basic domains, zinc-coordinating DNA binding domains, helix-turn-helix motifs, and beta scaffold factors with minor groove contacts. Particularly striking was the conservation of an AP-4 binding site within 100 nucleotides upstream of the transcription initiation site in both Aal-rpL34 and Aal-rpL8 genes. Comparison of Southern hybridization signals using probes from the 5' and 3'-ends of the 5.3 kb second intron and the cDNA suggested that the Ae. albopictus rpL34 gene most likely occurs as a single expressed copy per haploid genome with restriction enzyme polymorphisms in the upstream flanking DNA and the likely presence of one or more pseudogenes.

LBP-p40 binds DNA tightly through associations with histones H2A, H2B, and H4

Laminin binding protein precursor p40 (LBP-p40) was long believed to be located exclusively in the cytoplasm. We recently reported localization of epitope-tagged LBP-p40 to the nucleus tightly associated with nuclear structure as well as on ribosomes. In this paper, we analyze the interaction of LBP-p40 with DNA and nuclear proteins in vitro. LBP-p40 was found to bind to a double-stranded DNA cellulose column at moderate salt. However, when mixed with a high salt nuclear extract, LBP-p40 was eluted from the DNA cellulose column only at higher salt. An LBP-p40 affinity column indicated that both histone H1 and in particular the core histones associate with LBP-p40. Using recombinant core histone molecules fused with glutathione S-transferase (GST), we demonstrate that histones H2A, H2B, and H4 are capable of interacting with LBP-p40, whereas H3 is not. These results suggest that association of LBP-p40 with histones H2A, H2B, and H4 confers tight binding of LBP-p40 to chromatin DNA in the nucleus.

Characterization of a Schistosoma mansoni homologue of the gene encoding the breast basic conserved protein 1/L13 ribosomal protein

The Schistosoma mansoni gene sequence encoding the breast basic conserved protein 1/ribosomal protein L13 has been isolated from an adult worm cDNA library using the Expressed Sequence Tag strategy. The cDNA codes for a putative protein of 184 amino acids which is approximately 55% identical to other eukaryotic L13 ribosomal proteins. A PCR amplified genomic fragment containing the coding region of the gene was seen to possess only a single large intron interrupting the open reading frame. Studies of gene expression by RT-PCR showed the transcript is expressed in distinct stages of the parasite life cycle. The cDNA was also hybridized with an ordered cosmid library of S. mansoni and the identified cosmids were mapped to chromosomes 3 and W by chromosomal in situ suppression hybridization.

Differential gene expression in apoptosis: identification of ribosomal protein 23K, a cell proliferation inhibitor

Gene expression during the camptothecin-induced apoptotic death of human leukemic U937 cells and mouse T-cell hybridoma QW4.1 cells was studied by the mRNA differential display technique. Ten clones were confirmed to be differentially expressed, nine of which encoded novel sequences. One clone, U3.2, was induced approximately 10-fold in camptothecin-treated cells and was found to be identical to a highly basic 23-kDa human protein which contains basic leucine zipper-like motifs and has recently been identified as the human homologue of the rat ribosomal protein L13a. Northern blot analysis revealed a major mRNA of approximately 0.9 kb and a minor mRNA of approximately 1.3 kb. Overexpression of a full-length 23K cDNA, tagged with a FLAG sequence, in COS-7 cells revealed a predominantly nucleolar localization and the absence of any 23K protein from the cytoplasm. Subsequent transfection studies, using antisense phosphorothioate-modified oligonucleotides, revealed that inhibition of 23K expression results in an increased cell proliferation and greater sensitivity of U937 cells to the effects of camptothecin-induced cell death. Upregulation of 23K expression using a cDNA construct resulted in a decrease in cell proliferation and growth arrest, suggesting a role for 23K protein as a proliferation checkpoint following a cellular insult.

Triplet repeat-containing ribosomal protein L14 gene in immortalized human endothelial cell line (t-HUE4)

A cDNA encoding human 60S ribosomal subunit protein L14 (hRL14) was isolated from a human immortal endothelial cell line, t-HUE4. This cell line was established via a series of cell lines cultured in a serum-free and a protein-free medium, and a directional cDNA library has been constructed and screened in search for the genes modulating protein synthesis machinery in cell proliferation. A putative full-length clone with an open reading frame of 220 amino acids; predicted molecular weight of 23.6 kDa. A significant identity for hRL14 was observed with rat RL14 (85% identity), with exception of COOH-terminal region, but not with any eukaryote amino acid sequences so far deposited to database. The typical features of ribosomal proteins were observed in hRL14, as seen in nuclear targeting sequences necessary for the transport from cytoplasm to nucleolus, a bZIP like (basic region-leucine zipper) element for the binding to rRNA, and the internal repeat sequences; the pentapeptide QKA(A/S)X. The COOH-terminal region of the transcripts contained fifteen triplet repeats (GCT; alanine) at nucleotide 465 to 509, which is significantly expanded compared to the rat RL14. However, the repeat number was all the same among the normal human endothelial cell line and the cell lines established in the course of t-HUE4 establishment. A single band with about 800 bases was identified by Northern blot analysis without tissue specificity. This GCT repeat was found to be one of the longest uninterrupted repeats in a coding sequence, which were associated with the highest degree of polymorphism.

Eukaryotic gene expression: metabolite control by amino acids

Our understanding of the metabolite control in mammalian cells lags far behind that in prokaryotes. This is particularly true for amino-acid-dependent gene expression. Few proteins have been identified for which synthesis is selectively regulated by amino-acid availability, and the mechanisms for control of transcription and translation in response to changes in amino-acid availability have not yet been elucidated. The intimate relationship between amino-acid supply and the fundamental cellular process of protein synthesis makes amino-acid-dependent control of gene expression particularly important. Future studies should provide important insight into amino-acid and other nutrient signaling pathways, and their impact on cellular growth and metabolism.

Differential gene expression during early murine yolk sac development

The visceral yolk sac (VYS), composed of extraembryonic mesoderm and visceral endoderm, is the initial site of blood cell development and serves important nutritive and absorptive functions. In the mouse, the visceral endoderm becomes a morphologically distinct tissue at the time of implantation (E4.5), while the extraembryonic mesoderm arises during gastrulation (E6.5-8.5). To isolate genes differentially expressed in the developing yolk sac, polymerase chain reaction (PCR) methods were used to construct cDNA from late primitive streak to neural plate stage (E7.5) murine VYS mesoderm and VYS endoderm tissues. Differential screening led to the identification of six VYS mesoderm-enriched clones: ribosomal protein L13a, the heat shock proteins hsc 70 and hsp 86, guanine-nucleotide binding protein-related gene, cellular nucleic acid binding protein, and alpha-enolase. One VYS endoderm-specific cDNA was identified as apolipoprotein C2. In situ hybridization studies confirmed the differential expression of these genes in E7.5 yolk sac tissues. These results indicate that representative cDNA populations can be obtained from small numbers of cells and that PCR methodologies permit the study of gene expression during early mammalian postimplantation development. While all of the mesoderm-enriched genes were ubiquitously expressed in the embryo proper, apolipoprotein C2 expression was confined to the visceral endoderm. These results are consistent with the hypothesis that at E7.5, the yolk sac endoderm provides differentiated liver-like functions, while the newly developing extraembryonic mesoderm is still a largely undifferentiated tissue.

A unique tumor antigen produced by a single amino acid substitution

Mice immunized against a cancer recognize antigens unique to that cancer, but the molecular structures of such antigens are unknown. We isolated CD4+ T cell clones recognizing an antigen uniquely expressed on the UV-induced tumor 6132A; some clones inhibited the growth of tumors bearing the specific antigen. A T cell hybridoma was used to purify this antigen from nuclear extracts by RP-HPLC and SDS-PAGE using T cell immunoblot assays. A partial amino acid sequence was nearly identical to a sequence in ribosomal protein L9. The cDNA sequence of L9 from 6132A PRO cells differed from the normal sequence at one nucleotide; this mutation encoded histidine instead of leucine at position 47. A synthetic peptide containing this mutation was over 1000-fold more stimulatory of T cells than was the wild-type peptide. These results indicate that this unique tumor antigen is derived from a single amino acid substitution in a cellular protein.