Proposed uniform nomenclature for mammalian ribosomal proteins

Lyar, a cell growth-regulating zinc finger protein, was identified to be associated with cytoplasmic ribosomes in male germ and cancer cells

Translational control is a basic mechanism for gene regulation in cells and important for tissue growth and development in mammals. Deregulation of the mechanism thus causes diseases such as cancer. Considering the importance of the ribosome as a factory of polypeptide synthesis, some new factors have been expected to be associated with the ribosome and involved in translational control. Our proteomic survey for these factors identified a zinc finger protein, Lyar, in cytoplasmic ribosomes of the rodent testis. Subcellular fractionation of the testis provided data supporting association of Lyar with ribosomes. Lyar was then suggested to be included in the 60S large subunit, but not in polysomes, by ultracentrifugation of testicular ribosomes. While analysis of tissue distribution of Lyar has indicated its testis-predominant expression, Lyar mRNA was expressed in the cancer cells originated from tissues other than testis, and Lyar promoted proliferation of NIH-3T3 cells. Furthermore, translation was increased by Lyar in vitro, pointing out the first experimental link between this protein and translation. Taken together, Lyar seems to be a new player in translational control and a potential target for cancer therapy.

Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae

During the assembly process of ribosomal subunits, their structural components, the ribosomal RNAs (rRNAs) and the ribosomal proteins (r-proteins) have to join together in a highly dynamic and defined manner to enable the efficient formation of functional ribosomes. In this work, the assembly of large ribosomal subunit (LSU) r-proteins from the eukaryote S. cerevisiae was systematically investigated. Groups of LSU r-proteins with specific assembly characteristics were detected by comparing the protein composition of affinity purified early, middle, late or mature LSU (precursor) particles by semi-quantitative mass spectrometry. The impact of yeast LSU r-proteins rpL25, rpL2, rpL43, and rpL21 on the composition of intermediate to late nuclear LSU precursors was analyzed in more detail. Effects of these proteins on the assembly states of other r-proteins and on the transient LSU precursor association of several ribosome biogenesis factors, including Nog2, Rsa4 and Nop53, are discussed.

Active regulator of SIRT1 is required for ribosome biogenesis and function

Active regulator of SIRT1 (AROS) binds and upregulates SIRT1, an NAD(+)-dependent deacetylase. In addition, AROS binds RPS19, a structural ribosomal protein, which also functions in ribosome biogenesis and is implicated in multiple disease states. The significance of AROS in relation to ribosome biogenesis and function is unknown. Using human cells, we now show that AROS localizes to (i) the nucleolus and (ii) cytoplasmic ribosomes. Co-localization with nucleolar proteins was verified by confocal immunofluorescence of endogenous protein and confirmed by AROS depletion using RNAi. AROS association with cytoplasmic ribosomes was analysed by sucrose density fractionation and immunoprecipitation, revealing that AROS selectively associates with 40S ribosomal subunits and also with polysomes. RNAi-mediated depletion of AROS leads to deficient ribosome biogenesis with aberrant precursor ribosomal RNA processing, reduced 40S subunit ribosomal RNA and 40S ribosomal proteins (including RPS19). Together, this results in a reduction in 40S subunits and translating polysomes, correlating with reduced overall cellular protein synthesis. Interestingly, knockdown of AROS also results in a functionally significant increase in eIF2α phosphorylation. Overall, our results identify AROS as a factor with a role in both ribosome biogenesis and ribosomal function.

Identification of human, rat and chicken ribosomal proteins by a combination of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry

To identify the exact spot position of human, rat and chicken ribosomal proteins (RP) separated by two-dimensional polyacrylamide gel electrophoresis (2-DE), a 2-DE system was designed to separate RP with a pI>8.6 according to their charge in the first dimension and to their molecular mass in the second dimension. Individual proteins were excised from the gels and identified by mass spectrometry after digestion by trypsin. In addition, a mixture of purified RP from these three species was also analyzed by tandem mass tag spectrometry. By combining those two methods 74 RP from human, 76 from rat and 67 from chicken were identified according to the nomenclature initially defined for rat liver RP and by using the Swiss-Prot/trEMBL databases. Whereas human and rat RP were well described, most of RP from chicken were not characterized in databases, since 35 out of 67 chicken RP identified in this study were not listed yet. We propose here the first comprehensive description of chicken RP and their comparison to those from human and rat.

Functional analysis of structural motifs in dicistroviruses

The family Dicistroviridae is composed of positive-stranded RNA viruses which have monopartite genomes. These viruses carry genome-linked virus proteins (VPg) and poly (A) tails. The 5' untranslated region (UTR) is approximately 500 nucleotides and contains an internal ribosome entry site (IRES). These features resemble those of vertebrate picornaviruses, but dicistroviruses have other distinct characteristics. Picornaviruses have a single large open reading frame (ORF) encoding the capsid proteins at the 5'-end and the replicases at the 3'-end. In contrast, dicistroviruses have two nonoverlapping ORFs. The 5'-proximal ORF encodes the replicases and the 3'-proximal ORF encodes the capsid proteins. Usually, positive-stranded viruses which have capsid protein genes in the 3' part of the genome produce subgenomic RNA for synthesis of the capsid proteins, because abundant quantities of the capsid proteins are required for the viral replication cycle. In dicistroviruses, translation of the capsid proteins is controlled by an additional IRES. This IRES is located in the intergenic region (IGR) between the replicase and capsid coding regions, and mediates the initiation of translation for the capsid proteins. The IGR-IRES has a multiple stem-loop structure containing three pseudoknots. We describe the characteristics of dicistroviruses, including the RNA elements and viral proteins.

The ribosomal protein genes and Minute loci of Drosophila melanogaster

A combined bioinformatic and genetic approach was used to conduct a systematic analysis of the relationship between ribosomal protein genes and Minute loci in Drosophila melanogaster, allowing the identification of 64 Minute loci corresponding to ribosomal genes.

Background

Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes.

Results

We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci.

Conclusion

This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome.

Ribosomal protein gene regulation: what about plants?

The ribosome is an intricate ribonucleoprotein complex with a multitude of protein constituents present in equimolar amounts. Coordination of the synthesis of these ribosomal proteins (r-proteins) presents a major challenge to the cell. Although most r-proteins are highly conserved, the mechanisms by which r-protein gene expression is regulated often differ widely among species. While the primary regulatory mechanisms coordinating r-protein synthesis in bacteria, yeast, and animals have been identified, the mechanisms governing the coordination of plant r-protein expression remain largely unexplored. In addition, plants are unique among eukaryotes in carrying multiple (often more than two) functional genes encoding each r-protein, which substantially complicates coordinate expression. A survey of the current knowledge regarding coordinated systems of r-protein gene expression in different model organisms suggests that vertebrate r-protein gene regulation provides a valuable comparison for plants.

Ribosomal proteins cross-linked to the initiator AUG codon of a mRNA in the translation initiation complex by UV-irradiation

Eukaryotic ribosomal proteins constituting the binding site for the initiator codon AUG on the ribosome at the translation initiation step were investigated by UV-induced cross-linking between protein and mRNA. The 80S-initiation complex was formed in a rabbit reticulocyte cell-free system in the presence of sparsomycin with radiolabeled Omega-fragment as a template, which was a 73-base 5'-leader sequence of tobacco mosaic virus RNA having AUG at the extreme 3'-terminal end and extended with 32pCp. Two radioactive peaks were sedimented by sucrose gradient centrifugation, one being the 80S initiation complex formed at the 3'-terminal AUG codon, and the other presumably a "disome" with an additional 80S ribosome bound at an upstream AUU codon, formed when Omega-fragment was incubated with sparsomycin [Filipowicz and Henni (1979) Proc. Natl. Acad. Sci. USA 76, 3111-3115]. Cross-links between ribosomal proteins and the radiolabeled Omega-fragment were induced in situ by UV-irradiation at 254 nm. After extensive nuclease digestion of the complexes, ribosomal proteins were separated by two-dimensional gel electrophoresis. Autoradiography identified the proteins S7, S10, S25, S29, and L5 of the 80S initiation complex and S7, S25, S29 and L5 of that in the disome as 32P-labeled proteins. Together with the results of cross-linking experiments of other investigators and recently solved crystal structures of prokaryotic ribosomes, the spatial arrangement of eukaryotic ribosomal proteins at the AUG-binding domain is discussed.

Alteration of ribosomal protein maps in herpes simplex virus type 1 infection

At present, the effect of herpes simplex virus infection on the entire proteomes of infected cells is very poorly documented. Following several studies performed over the past few years, the modifications of a sub-cellular fraction induced by herpes simplex virus type 1 can be documented. These studies were performed in order to characterize the virally-induced modifications of a major component of the translational apparatus, the ribosomes. The very basic nature of most of the ribosomal proteins renders them very difficult to separate using isoelectric focusing (IEF). Therefore these studies were achieved using several different but related two-dimensional electrophoretic systems which allowed several two-dimensional ribosomal protein maps to be built. Comparison of the ribosomal protein maps built from non-infected cells with those built from infected cells demonstrated that infection by herpes simplex virus type 1 (HSV-1) induces important modifications of ribosomes: (i) non-reversible phosphorylation of ribosomal protein S6; (ii) unusual phosphorylation of several proteins of the small and the large subunits; and (iii) association of viral and cellular proteins to the ribosomal fraction. An overview of these published studies is presented in this review.

Interaction of mammalian mitochondrial ribosomes with the inner membrane

All of the products of mitochondrial protein biosynthesis in animals are hydrophobic proteins that are localized in the inner membrane. Hence, it is possible that the synthesis of these proteins could occur on ribosomes associated with the inner membrane. To examine this possibility, inner membrane and matrix fractions of bovine mitochondria were examined for the presence of ribosomes using probes for the rRNAs. Between 40 and 50% of the ribosomes were found to fractionate with the inner membrane. About half of the ribosomes associated with the inner membrane could be released by high salt treatment, indicating that they interact with the membrane largely through electrostatic forces. No release of the ribosome was observed upon treatment with puromycin, suggesting that the association observed is not due to insertion of a nascent polypeptide chain into the membrane. A fraction of the ribosomes remained with residual portions of the membranes that cannot be solubilized in the presence of Triton X-100. These ribosomes may be associated with large oligomeric complexes in the membrane.

Characterization by two-dimensional gel electrophoresis of host proteins whose synthesis is sustained or stimulated during the course of herpes simplex virus type 1 infection

Herpes simplex virus type 1 (HSV-1) gene expression is concomitant with a selective shutoff of host protein synthesis. While the synthesis of the vast majority of cellular proteins is inhibited immediately after infection, several cellular proteins continue to be synthesized, even during the late phase of infection. Because these cellular proteins may intervene in the life cycle of the virus, we undertook two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) analyses to evaluate the proportion of cellular proteins that is represented by these particular proteins. Human cells were infected with HSV-1. At different times after infection, proteins were labeled with 35S just prior to harvesting. The rate of synthesis of a set of 183 acidic host proteins, as well as that of ribosomal proteins, was measured during the course of infection, after separation by 2-D PAGE. As expected, HSV-1 induces a strong inhibition of host protein synthesis immediately after infection. However, the synthesis of basic ribosomal proteins and that of an unexpected high proportion of the sub-set of cellular proteins analyzed is sustained or stimulated during HSV-1 infection. A 2-D PAGE analysis outlining the expression patterns of these proteins at different times of infection is presented.

Identification of insulin-induced sites of ribosomal protein S6 phosphorylation in Drosophila melanogaster

Insulin treatment of Drosophila melanogaster Kc 167 cells induces the multiple phosphorylation of a Drosophila ribosomal protein, as judged by its decreased electrophoretic mobility on two-dimensional polyacrylamide gels. The extent to which insulin induces this response is potentiated by cycloheximide and blocked by pretreatment with rapamycin. Isolation and mass spectrometric analysis revealed that the multiply phosphorylated protein was the larger of two Drosophila melanogaster orthologues of mammalian 40S ribosomal protein S6, termed here DS6A. Proteolytic cleavage of DS6A derived from stimulated Kc 167 cells with the endoproteinase Lys-C released a number of peptides, one of which contained all the putative phosphorylation sites. Conversion of phosphoserines to dehydroalanines with Ba(OH)(2) showed that the sites of phosphorylation reside at the carboxy terminus of DS6A. The sites of phosphorylation were identified by Edman degradation after conversion of the phosphoserine residues to S-ethylcysteine as Ser(233), Ser(235), Ser(239), Ser(242), and Ser(245). Finally, phosphopeptide mapping of individual phosphoderivatives, isolated from two-dimensional polyacrylamide gels, indicated that DS6A phosphorylation, in analogy to mammalian S6 phosphorylation, appears to proceed in an ordered fashion. The importance of these observations in cell growth and development is discussed.

Identification of a mammalian mitochondrial homolog of ribosomal protein S7

Bovine mitochondrial small subunit ribosomal proteins were separated by two-dimensional electrophoresis. The region containing the most basic protein(s) was excised and the protein(s) present subjected to in-gel digestion with trypsin. Electrospray tandem mass spectrometry was used to provide sequence information on some of the peptide products. Searches of the human EST database using the sequence of the longest peptide analyzed indicated that this peptide was from the mammalian mitochondrial homolog of prokaryotic ribosomal protein S7 (MRP S7(human)). MRP S7(human) is a 28-kDa protein with a pI of 10. Significant homology to bacterial S7 is observed especially in the C-terminal half of the protein. Surprisingly, MRP S7(human) shows less homology to the corresponding mitochondrial proteins from plants and fungi than to bacterial S7.

Nucleolin interacts with several ribosomal proteins through its RGG domain

Nucleolin is one of the major nonribosomal proteins of the nucleolus. Through its four RNA-binding domains, nucleolin interacts specifically with pre-rRNA as soon as synthesis begins, but it is not found in mature cytoplasmic ribosomes. Nucleolin is able to shuttle between the cytoplasm and the nucleus. These data suggest that nucleolin might be involved in the nucleolar import of cytoplasmic components and in the assembly of pre-ribosomal particles. Here we show, using two-dimensional blots in a ligand blotting assay, that nucleolin interacts with 18 ribosomal proteins from rat (14 and 4 from the large and small subunit, respectively). The C-terminal domain of nucleolin (p50) interacts with 10 of these identified ribosomal proteins. In vitro binding assays show that the glycine-arginine rich domain of nucleolin (RGG domain) is sufficient for the interaction with one of these proteins. Interestingly, most of the proteins that interact with p50 belong to the core ribosomal proteins, which are resistant to extraction with high salt concentration. These findings suggest that nucleolin might be involved in the nucleolar targeting of some ribosomal proteins and in their assembly within pre-ribosomal particles.

Phosphorylation of ribosomal protein L30 after herpes simplex virus type 1 infection

In addition to an irreversible stimulation of S6 ribosomal protein phosphorylation, there is a modification of a subset of ribosomal proteins by phosphorylation after herpes simplex virus type 1 (HSV-1) infection. Moreover, in the course of this infection, three additional phosphorylated proteins can be extracted from ribosomes and separated by two-dimensional electrophoresis (2-DE) of total ribosomal proteins. One of them exhibits an identical molecular mass to L30, while being more acidic. This protein is phosphorylated on serine residues. The kinetics of appearance of this protein in the ribosomal fraction correlated with a decrease in L30 staining, as shown by 2-DE. Determination of the N-terminal amino acid sequence of this extra phosphoprotein and of L30-derived peptides demonstrated the identity of these two proteins.

Purification, primary structure and molecular cloning of a rat ribosomal protein showing homology with yeast ribosomal protein YL34

1. A new 17-kDa mammalian ribosomal protein (PR17) was purified to homogeneity from the rat exocrine pancreas. The purification procedure was based on acidic extraction of a heat-denatured homogenate, ammonium-sulfate precipitation, hydrophobic chromatography on phenyl-Sepharose and analytical reverse-phase HPLC on mu Bondapak C18. Fractions of interest were collected using an antiserum directed against the first (1-14) moiety of somatostatin (1-28). 30 micrograms pure RP17 were obtained from 1 g fresh pancreas. 2. A short 111-b cDNA encoding RP17 was amplified from rat pancreatic first-strand cDNA template by using two 64-fold degenerate heptadecamer primers in the DNA-polymerase-chain reaction. From the sequence of amplified cDNA, an unambiguous oligonucleotide probe was designed to screen a rat pancreatic cDNA library. A cDNA clone coding for RP17 was isolated, whose nucleotide sequence, with an open reading frame coding for 155 amino acids (molecular mass of 17,199 Da), confirmed the partial amino acid sequences directly obtained from the purified protein. 3. Northern-blot analysis showed that a similar 0.75-kb transcript was present in rat pancreas, in the rat pancreatic acinar cell line AR 4-2J and in the human neuroblastoma cell-line NB-OK-1, the highest level being in the latter two preparations, despite similar levels of RP17 in all three preparations, as tested with a rabbit antiserum directed against purified RP17. 4. The N-terminal sequence of both RP17 and the ribosomal protein YL43 from Saccharomyces cerevisiae (39 amino acid residues) showed a high degree of identity (77%), indicating that RP17 is a mammalian homolog of yeast ribosomal protein YL43.

Cloning and sequencing a cDNA encoding human ribosomal protein S25

A full-length cDNA clone has been isolated from a cDNA library prepared from mRNA of adriamycin-resistant human leukemia HL60 cells. The nucleotide sequence of this cDNA has been determined and the protein coded for by the gene identified. The cDNA encodes a polypeptide of 125 amino acids (aa) with a deduced Mr of 13750. The deduced aa sequence of this protein has 56% homology to yeast ribosomal protein S31. Western-blot analysis using antibodies directed against a synthetic peptide based on the deduced aa sequence identifies the gene product as the human ribosomal protein S25.

The primary structure of rat ribosomal proteins P0, P1, and P2 and a proposal for a uniform nomenclature for mammalian and yeast ribosomal proteins

The covalent structures of rat ribosomal proteins P0, P1, and P2 were deduced from the sequences of nucleotides in recombinant cDNAs. P0 contains 316 amino acids and has a molecular weight of 34,178; P1 has 114 residues and a molecular weight of 11,490: and P2 has 115 amino acids and a molecular weight of 11,684. The rat P-proteins have a near identical (16 of 17 residues) sequence of amino acids at their carboxyl termini and are related to analogous proteins in other eukaryotic species. A proposal is made for a uniform nomenclature for rat and yeast ribosomal proteins.

rig encodes ribosomal protein S15. The primary structure of mammalian ribosomal protein S15

rig, a gene originally isolated from a rat insulinoma cDNA library, codes for a basic 145 amino acid protein [( 1986) Diabetes 35, 1178-1180]. Here we show that the immunoreactivity to a monoclonal antibody against the deduced rig protein and the translation product of rig mRNA comigrated with ribosomal protein S15. The amino acid sequence of ribosomal protein S15 purified from rat liver coincided with that deduced from the nucleotide sequence of rig mRNA, but there were indications that the initiator methionine was removed and the succeeding alanyl residue was monoacetylated. From these results, we conclude that the product of rig is ribosomal protein S15.

Nucleotide sequence of mouse L19 ribosomal protein cDNA isolated in screening with tre oncogene probes

A cDNA library was prepared from cytoplasmic poly(A)RNA from mouse NIH-3T3 cells carrying a transfected human tre oncogene. Screening with tre gene probes identified a tre cDNA clone 11-4 and a co-purifying weakly hybridizing cDNA clone 11-5. The 11-5-specific RNA was expressed in both nontransfected and tre-transfected NIH-3T3 cells, showing it is of mouse rather than tre gene origin. Its nucleotide sequence was 717 bp long and contained, starting from the first nucleotide, an open reading frame of 588 bp followed by a 3' noncoding region and 26 A residues at the 3' terminus. Comparison with the GenBank data base revealed 93.7% homology with cDNA encoding the rat L19 ribosomal protein. Furthermore, the 196-amino-acid polypeptide deduced from 11-5 was of the same length and contained only one amino acid difference compared with the rat L19 protein. Comparison with the weakly hybridizing tre gene probe showed stretches of homology that were, however, too short to be taken into consideration. We conclude that the 11-5 sequence encodes the mouse L19 ribosomal protein.

Herpes simplex virus type-1-induced stimulation of ribosomal protein S6 phosphorylation is inhibited in neomycin-treated human epidermoid carcinoma 2 cells and in ras-transformed cells

Neomycin, an inhibitor of inositol phospholipid turnover, prevents Herpes-simplex-virus-type-1 (HSV-1)-induced stimulation of ribosomal protein S6 phosphorylation, but does not impair the S6 phosphorylation induced by serum. Long-term treatment with phorbol 12-myristate 13-acetate, which down-regulates protein kinase C activity, does not inhibit virus-induced S6 phosphorylation. In ras-transformed cells, S6 phosphorylation is not stimulated after HSV-1 infection. These results suggest that activation of the inositol phospholipid pathway is involved in the HSV-1-induced stimulation of S6 phosphorylation. However, protein kinase C activation does not appear to be necessary for HSV-1-induced S6 phosphorylation.

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

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

A cDNA encoding human ribosomal protein S24

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

Immunological localization of ribosomes in striated rat muscle. Evidence for myofibrillar association and ontological changes in the subsarcolemmal:myofibrillar distribution

Ribosome distribution in skeletal-muscle fibres was investigated immunohistochemically by using polyclonal antibodies raised against large-ribosomal-subunit proteins isolated from rat liver. Immunoblot analysis showed the antibodies to recognize five major proteins of the large subunit; these were identified as L4, L6, L7, L15 and L17 by two-dimensional electrophoresis. Immunohistochemistry of frozen rat skeletal-muscle sections showed staining of both the subsarcolemmal and intermyofibrillar cytoplasm. A distinct banding pattern was observed, and when peroxidase and phase-contrast images of the same field were compared by image analysis the anti-ribosome staining was found to correspond to the A-bands. These results suggest that a proportion of muscle ribosomes are present in the myofibrillar cytoplasm in a regular fashion, possibly associated with myosin. Densitometric analysis of the peroxidase immunostaining showed that the ratio of myofibrillar to sub-sarcolemmal ribosomal material was lower in muscle from 51-day-old rats compared with those from 14-day-old animals.

Modification of the accessibility of ribosomal proteins after elongation factor 2 binding to rat liver ribosomes and during translocation

Free- and EF-2-bound 80 S ribosomes, within the high-affinity complex with the non-hydrolysable GTP analog: guanylylmethylenediphosphonate (GuoPP(CH2)P), and the low-affinity complex with GDP, were treated with trypsin under conditions that modified neither their protein synthesis ability nor their sedimentation constant nor the bound EF-2 itself. Proteins extracted from trypsin-digested ribosomes were unambiguously identified using three different two-dimensional gel electrophoresis systems and 5 S RNA release was checked by submitting directly free- and EF-2-bound 80 S ribosomes, incubated with trypsin, to two-dimensional gel electrophoresis. Our results indicate that the binding of (EF-2)-GuoPP[CH2]P to 80 S ribosomes modified the behavior of a cluster of five proteins which were trypsin-resistant within free 80 S ribosomes and trypsin-sensitive within the high-affinity complex (proteins: L3, L10, L13a, L26, L27a). As for the binding of (EF-2)-GDP to 80 S ribosomes, it induced an intermediate conformational change of ribosomes, unshielding only protein L13a and L27a. Quantitative release of free intact 5 S RNA which occurred in the first case but not in the second one, should be related to the trypsinolysis of protein(s) L3 and/or L10 and/or L26. Results were discussed in relation to structural and functional data available on the ribosomal proteins we found to be modified by EF-2 binding.

Ribosome and protein synthesis modifications after infection of human epidermoid carcinoma cells with herpes simplex virus type 1

Modifications of ribosomes have been investigated in human epidermoid carcinoma-2 cells at different stages of herpes simplex virus type 1 infection. Very early in infection, there is an increase in ribosomal protein S6 phosphorylation even in the absence of serum. The same result is obtained in the presence of actinomycin D. At early infection time, ribosomal proteins S2, S3a and Sa are newly phosphorylated. At early and early-late times, three phosphorylated non-ribosomal proteins (v1, v2 and v3) are differently associated temporally to ribosomes. Analyses of proteins extracted from 40S subunits, 80S ribosomes and polysomes show that v1 and v2 are distributed differently among the different ribosomal populations. S6 phosphopeptides were found to be identical after serum stimulation and after viral infection. In every case phosphoserine and phosphothreonine were identified in S6. Only phosphoserine was found in other phosphorylated proteins. Our results indicate that herpes simplex virus type 1 is able to modify pre-existing ribosomes: (i) by stimulating a pre-existing kinase for S6 phosphorylation even in the absence of serum and of viral genome expression; (ii) by inducing new specific kinase activity(ies); and (iii) by association of new, phosphorylated proteins to ribosomes. These ribosomal modifications are correlated with changes in protein synthesis, as shown by two-dimensional electrophoretic analyses of newly synthesized 35S-labelled proteins.

Structural differences between active and inactive mammalian 60S ribosomal subunits. Circular dichroism and electric birefringence studies

The structure and conformation of different active and inactive forms of the 60S rat liver ribosomal subunits have been analyzed by electric birefringence and circular dichroism. These studies show the following: 1) When a phosphate buffer is used instead of a triethanolamine buffer, there are major changes in RNA stacking, RNA-protein interactions, and particle orientation and conformation with no concomitant loss in ribosome activity. 2) The inactivated subunits by K(+)-depletion exhibit the same electro-optical and near-UV CD behaviour than the active subunits in phosphate buffer. 3) Inactivation by EDTA-treatment leads to drastic changes in RNA structure, RNA-protein interactions and subunit conformation; the 60S particles behave like free RNA, indicating the absence of any stabilization of rRNA by ribosomal proteins. 4) The inactivation of subunits by depletion of either monovalent or divalent cations is accompanied by a net decrease of the alpha-helicity of the ribosomal proteins. 5) The transition from active to inactive form of 60S subunits may involve protein modifications, likely dependent on a specific array of cations. 6) RNA has a certain degree of liberty within the subunits and one can suppose that this property is responsible for the flexible structure of ribosome.

Heterogeneity of ribosomal autoantibodies from human, murine and canine connective tissue diseases

Antiribosomal auto-antibodies (anti-Rib.Ab) have been studied in connective tissue diseases (human, dog and mouse) by immunoblotting after one-dimensional (1D) or two-dimensional (2D) gel electrophoresis of rat ribosomes. Anti-Rib.Ab could be found in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and other connective tissue diseases (progressive systemic sclerosis, PSS; Sjögren syndrome, SjS; mixed connective tissue disease, MCTD; and dermatomyositis, DM with the frequencies 41.7%, 54.6% and 33%, respectively. Immunoblotting after 1D gel electrophoresis showed the great heterogeneity of ribosomal proteins recognized by the anti-Rib.Ab. In the SLE, however, the most frequent antibodies stained bands of the 40S subunit: 30 kDa (34% of positive sera), 19.5 kDa (24.5%) and 43 kDa (17%). In RA, the 25-kDa band of the 60S subunit was the most common (54% of positive sera). In the other human connective tissue diseases, there was no particular predominance. In the MRL/1, anti-Rib.Ab were very frequent (92.6%). The 43-kDa band of the 40S subunit was found in 100% of positive sera. Seventeen out of nineteen dogs with SLE gave positive results on immunoblot, and all of them stained the 43-kDa band of the 40S subunit. 2D gel electrophoresis gave identification of Po, L7, L5, Sb, S19, S13 and L2 proteins in SLE, S3 and SjS, L35a and L37a in RA, and L7, S6 and/or L7a in MRL/1.

Protein-RNA crosslinking in the subunits of the cytoplasmic ribosome of Tetrahymena thermophila

Use of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide to introduce RNA-protein crosslinks in the 40S and 60S subunits of the cytoplasmic ribosome of Tetrahymena thermophila is described, and proteins linked covalently to 17S and 26S ribosomal RNAs are identified. RNA-protein crosslinking is accompanied by extensive dimerization and aggregation of ribosomal subunits probably due to formation of interparticle protein-protein crosslinks.

Ribosomal proteins of Tetrahymena thermophila. Correlation of one- and two-dimensional electrophoretic migration patterns and characterization of additional small and large subunit proteins

Further analysis of the protein complement of the cytoplasmic ribosome of the protozoon Tetrahymena thermophila has led to the identification and characterization of seven additional proteins, three in the small and four in the large subunit of this ribosome. Several of these proteins are poorly soluble or insoluble in the absence of high concentrations of urea and are not seen in the electrophoretic distribution patterns of ribosomal proteins in two-dimensional polyacrylamide gels unless 6 M urea is added to electrode buffers in contact with protein samples (first dimension) and first-dimension gels (second dimension). The migration patterns of the 40S and 60S subunits of the T. thermophila ribosome in one-dimensional polyacrylamide SDS gels and in two-dimensional gels prepared by means of the basic-acidic system of Kaltschmidt and Wittmann**, and the basic-SDS system of Zinker and Warner*** have been correlated.

Identification of the long ubiquitin extension as ribosomal protein S27a

Two proteins of unknown function are encoded by 3' in-frame extensions of ubiquitin genes. The polypeptides are synthesized as an additional 52 or 76-80 amino acids on the C terminus of ubiquitin, an unusual arrangement conserved in man, yeast and plants (J. Callis and R. Vierstra, personal communication). Although not homologous to each other or to ubiquitin, both extension proteins are highly basic and contain patterns of cysteine and histidine similar to those proposed to form 'zinc fingers'. The longer C-terminal extension protein (CEP80) is 30% lysine and arginine and, when denatured, behaves like a small cationic protein. Its properties after isolation in physiological conditions, however, suggested that CEP80 is part of an RNA-protein complex. Using the antibodies that confirmed the presence of CEP80 in eukaryotic cells, we show here that the protein is located on ribosomes. Immunoblotting of rat 40S subunit proteins specifically identifies CEP80 as ribosomal protein S27a.

Reconstitution of the active rat liver 60 S ribosomal subunit from different preparations of core particles and split proteins

Proteins extracted from the 60 S rat liver ribosomal subunit with 50% ethanol/0.5 M K Cl produced only a partial reactivation of the corresponding core particles. In contrast, the same split proteins were able to reactivate the core particles prepared with dimethyl-maleic anhydride (DMMA) to the same level as that observed using the DMMA-split proteins, i.e. 60-80% of the control according to the catalytic activities tested. Comparative analysis of the two split protein fractions showed only four common proteins: P1-P2, which alone restored part of the activities, especially the EF-2-dependent GTPase one, and L10a, L12, which must be responsible for the additional reactivation. The poor ability of the ethanol/KCl core particles to be reactivated was shown to be probably related to a conformational alteration which destabilized the 5 S RNA-protein complex. Proteins present in the ethanol/KCl wash of Saccharomyces cerevisiae 60 S subunits were found to be partly active in subunit reconstitution using rat liver DMMA core particles.

Identification of proteins of the 40 S ribosomal subunit involved in interaction with initiation factor eIF-2 in the quaternary initiation complex by means of monospecific antibodies

Monospecific polyclonal antibodies against seven proteins of the 40 S subunit of rat liver ribosomes were used to identify ribosomal proteins involved in interaction with initiation factor eIF-2 in the quaternary initiation complex [eIF-2 X GMPPCP X [3H]Met-tRNAf X 40 S ribosomal subunit]. Dimeric immune complexes of 40 S subunits mediated by antibodies against ribosomal proteins S3a, S13/16, S19 and S24 were found to be unable to bind the ternary initiation complex [eIF-2 X GMPPCP X [3H]Met-tRNAf]. In contrast, 40 S dimers mediated by antibodies against proteins S2, S3 and S17 were found to bind the ternary complex. Therefore, from the ribosomal proteins tested, only proteins S3a, S13/16, S19 and S24 are concluded to be involved in eIF-2 binding to the 40 S subunit.

Ribosomal proteins S2, S6, S10, S14, S15 and S25 are localized on the surface of mammalian 40 S subunits and stabilize their conformation. A study with immobilized trypsin

Trypsin immobilized on collagen membranes has been used to digest accessible ribosomal proteins of rat liver 40 S subunits. Six proteins (S2, S6, S10, S14, S15 and S25) have been found to be highly exposed on the surface of 40 S particles. They appear to be in close physical contact and localized in the same region of the subunit, most likely protruding at its surface. Electric birefringence reveals that digestion of these proteins results in unfolding of subunits: the birefringence of 40 S particles becomes negative, like that of RNA, the relaxation time undergoes a 15-fold decrease and the mechanism of orientation is drastically modified.

Primary structure of rat ribosomal protein L36a

The amino acid sequence of rat ribosomal protein L36a, which may form part of the peptidyl transferase center, was deduced from the sequence of nucleotides in a recombinant cDNA and confirmed from the amino-terminal amino acid sequence of the protein. Ribosomal protein L36a contains 105 amino acids (the amino-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 12,311. Hybridization of the cDNA to digests of nuclear DNA suggests that there are multiple copies of the L36a gene. Rat ribosomal protein L36a is homologous to a protein HL44 present in ribosomes of humans and protein 44 from Saccharomyces cerevisiae ribosomes.

Immunological homologies between yeast ribosomal protein L2 and rat liver ribosomal proteins L4 and L24

Polyclonal antibodies raised against ribosomal protein (r-protein) L2 of Schizosaccharomyces pombe were used to check for cross-reactions with total r-proteins of rat liver. Using this procedure, the rat liver r-proteins, L4 and L24, were identified as being immunologically related to yeast L2. In additional, homologies between rat liver L4 and L24 were detected. The possible implications for the regulation of r-protein synthesis are discussed.

Phosphorylation of ribosomal proteins during meiotic maturation and following activation in starfish oocytes: its relationship with changes of intracellular pH

An increased phosphorylation of ribosomal protein S6 has been shown to be correlated with an increase of intracellular pH (pHi) and with stimulation of protein synthesis in many systems. In this research changes in ribosome phosphorylation following hormone-induced meiotic maturation and fertilization or activation by ionophore A23187 were investigated in starfish oocytes. The hormone was found to stimulate, even in the absence of external Na+, the phosphorylation on serine residues of an Mr 31,000 protein identified as S6, as well as that of an acidic Mr 47,000 protein, presumably S1, on threonine residues. Phosphorylation of ribosomes was an early consequence of hormonal stimulation and did not decrease after completion of meiotic maturation. Fertilization or activation by ionophore of prophase-arrested oocytes also stimulated ribosome phosphorylation. Only S6 was labeled in this case, but to a lesser extent than upon hormone-induced meiotic maturation. Changes in pHi were monitored with ion-specific microelectrodes throughout meiotic maturation and following either fertilization or activation. The pHi did not change before germinal vesicle breakdown (GVBD) following hormone addition, but it increased before first polar body emission. It also increased following fertilization or activation by ionophore or the microinjection of Ca-EGTA. In all cases, alkalinization did not depend on activation of an amiloride-sensitive Na+/H+ exchanger. Microinjection of an alkaline Hepes buffer or external application of ammonia, both of which increased pHi, prevented unfertilized oocytes from arresting after formation of the female pronucleus and induced chromosome cycling. Phosphorylation of S6 was still observed following fertilization or induction of maturation when pHi was decreased by external application of acetate, a treatment which suppressed the emission of polar bodies. Protein synthesis increased in prophase-arrested oocytes after fertilization or activation. It also increased after ammonia addition, although this treatment did not stimulate S6 phosphorylation.

Localization of ribosomal proteins on the surface of mammalian 60S ribosomal subunits by means of immobilized enzymes. Correlation with chemical cross-linking data

Trypsin covalently bound on collagen membranes has been used to investigate the protein topography in eukaryotic 60S ribosomal subunits. Six proteins are highly exposed to the attack of the immobilized enzyme: L6, L7-L7a, L17, L24, and L31. They are located in two distinct regions, forming two bulges at the ribosomal surface; the first one consists of proteins L6 and L7-L7a, which are screening proteins degraded later, as L4, L14, L23a, and L29; the second one is formed by proteins L17, L24, and L31, which are shielding L19 and L22. L3, L5, L8, L11, L12, L26, L30, L34, and L37a, are located in a trough between the two bulges. L10, close to L5, appears to be more accessible than all these proteins. Several proteins are not degraded by trypsin, even for a very long time of incubation: L9, L13-L13a, L18, L18a, L21, L25, L27-L27a, L28, L32, L35, L35a, L36-L36a, and L38. The cross-linking data suggest that these latter proteins are mainly protected by the proteins located in the L6-L7-L7a region, and by the 28S RNA. A model of protein topography within the 60S rat liver subunits, based on protein accessibility and cross-linking data, is proposed.

Characterisation of the ribosomal binding site for eukaryotic elongation factor 2 by chemical cross-linking

Ribosomal complexes containing elongation factor 2 (EF-2) were formed by incubation of 80 S ribosomes in the presence of EF-2 and the non-hydrolysable GTP analogue GuoPP[CH2]P. The factor was covalently coupled to the ribosomal proteins located at the factor binding site, by treatment with bifunctional reagents. After isolation of the covalent EF-2.ribosomal protein complexes, the proteins were labelled with 125I and the introduced covalent links cleaved. The ribosomal proteins were identified by electrophoresis in two independent two-dimensional gel systems, followed by autoradiography. After cross-linking with bis(hydroxysuccinimidyl) tartrate (4 A between the reactive groups), protein S3/S3a, S7 and S11 were found as the major ribosomal proteins covalently linked to EF-2. The longer reagent, dimethyl 3,8-diaza-4,7-dioxo-5,6-dihydroxydecanbisimidate (11 A between the reactive groups), covalently coupled proteins S7, S11, L5, L13, L21, L23, L26, L27a and L32 to EF-2. After cross-linking with dimethyl suberimidate (9 A between the reactive groups) proteins S3/3a, S7, S11, L5, L8, L13, L21, L23, L26, L27a, L31 and L32 were identified as belonging to the EF-2-binding site. The results indicate that the ribosomal domain interacting with EF-2 is located on both the small and the large ribosomal subunit close to the subunit interface.

A comparison of accessibility of ribosomal proteins on free and membrane-bound ribosomes: the ribosomal proteins potentially involved in ribosome-membrane binding

The relative accessibility of rat liver ribosomal proteins to reductive methylation was examined using membrane-bound and free ribosomes. Comparisons indicated that 12-13 large ribosomal proteins are masked by ribosomal association with membranes. These consisted of L8, L10, L17, L26-28, L31 and L36, and probably also include L4, L5, L7 and L29. These proteins seem to surround a region centered about L3 and may partly define a ribosomal channel through which the nascent peptide emerges. Approx. 10-20% of the large ribosomal subunit surface area is shielded by the membrane.

Ion-exchange chromatography of ionic detergent-solubilized proteins: application to purification of rat parotid gland phosphoproteins including ribosomal protein S6

A method is described for separation of ionic detergent-solubilized proteins by ion-exchange chromatography. This method has been developed for purification of two phosphoproteins (Mr 19,000 and 30,000) from 32Pi-prelabeled, isoproterenol-stimulated rat parotid tissue and is based on the observation that, in the presence of urea and Nonidet-P40, ionic detergent-solubilized proteins can be adsorbed by ion exchangers according to their own charge. After adsorption, proteins were eluted with a stepwise gradient of NaCl in a urea-containing buffer. By the procedure described, the 30 kDa phosphoprotein was freed from other 32P-labeled substances; and it was identified as ribosomal protein S6 that was phosphorylated at some serine residues. The method is generally applicable and especially suited for preliminary purification of hydrophobic proteins subjected to analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

5S-rRNA-containing ribonucleoproteins from rabbit muscle and liver. Complex and partial primary structures

A 5S-rRNA-containing ribonucleoprotein was purified to homogeneity from a rabbit muscle extract through its affinity to phosphofructokinase-1 and then structurally characterized. This RNP was compared to the 5S-rRNA-containing ribonucleoprotein extracted from rabbit liver ribosomal 60S subunits with EDTA. Analytical gel filtration revealed a molecular mass of 70-80 kDa for both complexes. Gel electrophoresis of the ribosomal complex revealed three protein components, one migrating as a band of 35 kDa and two other small polypeptides of apparently 16.5 kDa and 17.5 kDa. In the sarcoplasmic RNP these small polypeptides were absent. However, besides a major component of 35 kDa, up to five slightly larger and smaller species of 31.5-36.5 kDa were detected. Despite this heterogeneity, only one N-terminal amino acid sequence was obtained for the isolated sarcoplasmic protein, suggesting a C-terminal heterogeneity of one single polypeptide. Within the first 46 amino acid residues no difference between the sequences of the isolated 35-kDa components of sarcoplasmic and ribosomal complexes was found. Homology criteria indicated that this component belongs to the ribosomal protein L5 family. The RNA was identified by complete enzymatic sequencing as 5S rRNA; it was also identical in both complexes and is strongly homologous to 5S rRNA of man. Both L5-5S-RNA complexes could be resolved by hydroxyapatite chromatography into three species still consisting of both protein and RNA. 5'-Terminal dephosphorylation experiments showed that this heterogeneity is exclusively due to the differing number (1-3) of 5'-terminal phosphates. The two additional low-molecular-mass proteins were stably associated to the ribosomal RNP at high salt concentrations in a stoichiometry of about 2:1. They were identified as the acidic phosphoproteins P2/P3 by N-terminal sequencing. High phosphate concentrations facilitated their dissociation from the L5-5S-RNA complex. For the sarcoplasmic L5-5S-RNA complex a hitherto unknown interaction with phosphofructokinase-1, affecting the enzymatic properties, was demonstrated.

Molecular cloning and nucleotide sequence of cDNA specific for rat ribosomal protein L5

cDNA clones specific for rat ribosomal protein L5, which is the protein moiety of 5S RNA protein particles, were isolated by using a mixture of tetradecamer deoxyribonucleotide probes reflecting the amino acid sequence of the N-terminal portion of L5. A cDNA clone (pRL5-1) lacking the 3'-terminal region of L5 was isolated by hybrid-selected translation and shown to be L5-specific by the identity of the deduced amino acid sequence and that of the N-terminus of protein L5. pRL5-1 was then used to select another clone (pRL5-2) by colony hybridization which contained the entire coding region, 3'-non-coding region and poly(A) addition signal. The nucleotide sequence of L5-specific cDNA was determined by using these two clones. It contained a total of 1069 base pairs: 123 base pairs in the 5'-non-coding region, 894 base pairs in the coding region and 52 base pairs in the 3'-non-coding region. The poly(A) addition signal appeared at the 33rd nucleotide after the termination codon. The amino acid sequence deduced from this nucleotide sequence consists of 296 amino acids. The homology of amino acid sequence between L5 and other 5S RNA-binding proteins is discussed.

5S RNA-protein complexes released by EDTA treatment of 60S ribosomal subunits of Tetrahymena thermophila

Treatment of large (60S) subunit of the cytoplasmic ribosome of the protozoa Tetrahymena thermophila with EDTA causes quantitative release of 5S rRNA associated with variable non quantitative amounts of one or more of 60S proteins L4, L15, L24, L31 and L41. The composition of the group of proteins released with 5S rRNA depends on both the molar ratio of EDTA and 60S subunits and the concentration of 60S subunits, in treatment mixtures.