A Comparison of the Proteins of Rat Skeletal Muscle and Liver Ribosomes by Two-Dimensional Polyacrylamide Gel Electrophoresis

Ribosome biogenesis and function in development and disease

Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.

Differential Paralog-Specific Expression of Multiple Small Subunit Proteins Cause Variations in Rpl42/eL42 Incorporation in Ribosome in Fission Yeast

Ribosomes within a cell are commonly viewed as biochemically homogenous RNA–protein super-complexes performing identical functions of protein synthesis. However, recent evidence suggests that ribosomes may be a more dynamic macromolecular complex with specialized roles. Here, we present extensive genetic and molecular evidence in the fission yeast S. pombe that the paralogous genes for many ribosomal proteins (RPs) are functionally different, despite that they encode the same ribosomal component, often with only subtle differences in the sequences. Focusing on the rps8 paralog gene deletions rps801d and rps802d, we showed that the mutant cells differ in the level of Rpl42p in actively translating ribosomes and that their phenotypic differences reside in the Rpl42p level variation instead of the subtle protein sequence difference between Rps801p and Rps802p. Additional 40S ribosomal protein paralog pairs also exhibit similar phenotypic differences via differential Rpl42p levels in actively translating ribosomes. Together, our work identifies variations in the Rpl42p level as a potential form of ribosome heterogeneity in biochemical compositions and suggests a possible connection between large and small subunits during ribosome biogenesis that may cause such heterogeneity. Additionally, it illustrates the complexity of the underlying mechanisms for the genetic specificity of ribosome paralogs.

Identification of Changing Ribosome Protein Compositions using Mass Spectrometry

The regulatory role of the ribosome in gene expression has come into sharper focus. It has been proposed that ribosomes are dynamic complexes capable of changing their protein composition in response to environmental stimuli. MS is applied to identify quantitative changes in the protein composition of S. cerevisiae 80S ribosomes in response to different environmental stimuli. Using quantitative MS, it is found that the paralog yeast ribosomal proteins RPL8A (eL8A) and RPL8B (eL8B) change their relative proportions in the 80S ribosome when yeast is switched from growth in glucose to glycerol. By using yeast genetics and polysome profiling, it is shown that yeast ribosomes containing either RPL8A or RPL8B are not functionally interchangeable. The quantitative proteomic data support the hypothesis that ribosomes are dynamic complexes that alter their composition and functional activity in response to changes in growth or environmental conditions.

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

Translation regulation by ribosomes: Increased complexity and expanded scope

The primary function of ribosomes is to decode mRNAs into polypeptide chains; however, this description is overly simplistic. Accumulating evidence shows that ribosomes themselves can affect the relative efficiency with which various mRNAs are translated and indicates that these effects can be modulated by ribosome heterogeneity. The notion that ribosomes have regulatory capabilities was elaborated more than a decade ago in the ribosome filter hypothesis. Various lines of evidence support this idea and have shown that the translation of some mRNAs is affected by discrete binding interactions with rRNA or ribosomal proteins. Recent work from our laboratory has demonstrated that base-pairing of the Hepatitis C Virus (HCV) internal ribosome entry site (IRES) to 18S rRNA is required for IRES function, but only in the context of more complex ribosomal interactions. The HCV IRES provides an example of the ribosome filter that involves multiple binding interactions between mRNAs and ribosomal subunits.

The ribosome filter hypothesis

A variety of posttranscriptional mechanisms affects the processing, subcellular localization, and translation of messenger RNAs (mRNAs). Translational control appears to occur primarily at the initiation rather than the elongation stage. It has been suggested that translation is mediated largely by means of a cap-binding/scanning mechanism. On the basis of recent findings, we propose here that differential binding of particular mRNAs to eukaryotic 40S ribosomal subunits before translation may also selectively affect rates of polypeptide chain production. In this view, ribosomal subunits themselves are considered to be regulatory elements or filters that mediate interactions between particular mRNAs and components of the translation machinery. Differences in these interactions affect how efficiently individual mRNAs compete for ribosomal subunits. These competitive interactions would depend in part on the complementarity between sequences in mRNA and rRNA, as well as on structural differences among ribosomes in different cell types. By these means, translation may either be enhanced through increased recruitment of ribosomes or inhibited through strong interactions that sequester mRNAs. We propose that ribosomal filters may be important in cell differentiation and describe experimental tests for the filter hypothesis.

Different sensitivity of recombinant Aspergillus niger phytase (r-PhyA) and Escherichia coli pH 2.5 acid phosphatase (r-AppA) to trypsin and pepsin in vitro

Proteolysis of two purified recombinant enzymes, namely, the Aspergillus niger phytase (r-PhyA) and the Escherichia coli pH 2.5 acid phosphatase (r-AppA), by pepsin and trypsin was investigated in this study. After r-PhyA and r-AppA were incubated with different concentrations of pepsin or trypsin, their residual phytase activities and amounts of inorganic phosphorus released from soybean meal were determined. Both enzymes retained more than 85% of their original activities at the trypsin/phytase ratios (w/w) 0.001 and 0. 005, while r-AppA and r-PhyA lost 60 and 20% of the original activity at the ratio of 0.01 or 0.025, respectively. In contrast, there was a 30% increase in phytase activity after r-AppA was incubated with pepsin at the ratios of 0.005 or 0.01. Meanwhile, r-PhyA lost 58 to 77% of its original activity under the same conditions. Trypsin and pepsin affected the hydrolysis of phytate phosphorus from soybean meal by r-AppA and r-PhyA in a similar way to their residual phytase activities. All of these in vitro proteolyses were confirmed by SDS-PAGE analysis. Our results demonstrate different sensitivities of r-AppA and r-PhyA to trypsin and pepsin, suggesting active trypsin resistant r-PhyA and pepsin resistant r-AppA polypeptides.

Ribosomal proteins of Thermomyces lanuginosus--characterisation by two-dimensional gel electrophoresis and differential disassembly

One- and two-dimensional gel electrophoresis were employed to characterise the proteins derived from the ribosomes of the thermophilic fungus Thermomyces lanuginosus. Approximately 32 (29 basic and 3 acidic) and 45 (43 basic and 2 acidic) protein spots were resolved from Th. lanuginosus small and large ribosomal subunits, respectively. The molecular weight of the small subunit proteins ranged from 9,800-36,000 Da with a number average molecular weight of 20,300 Da. The molecular weight range for the large subunit proteins was 12,000-48,500 Da with a number average molecular weight of 25,900 Da. Most proteins appeared to be present in unimolar amounts. These data are comparable with but not identical to those from other eukaryotic ribosomes. The sensitivities of the ribosomal proteins to increasing concentrations of NH4Cl were also evaluated by two-dimensional gel electrophoresis. Most ribosomal proteins were gradually released over a wide range of salt concentrations but some were preferentially enriched in one or two salt conditions.

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

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

Differentiation of rat myoblasts. Regulation of turnover of ribosomal proteins and their mRNAs

The regulation of ribosomal proteins (r-proteins) and their mRNAs (rp-mRNAs) was studied in the L6 myoblast, a mammalian cell line which can undergo myogenesis. Upon terminal differentiation, the rate of accumulation of mature ribosomes dropped to approximately 25% of the rate found in undifferentiated myoblasts. Despite the drop in the rate of ribosome accumulation and the rate of rRNA synthesis following terminal differentiation, the rate of r-protein synthesis remained constant. The excess r-protein synthesized in myotubes was quickly degraded. The levels of rp-mRNAs were assessed before and after differentiation. Over 90% of the rp-mRNAs were found on polysomes in both myoblasts and myotubes and represented similar fractions of total poly(A)-rich mRNA. The half-lives of the rp-mRNAs averaged approximately 11 h in both myoblasts and myotubes. In vitro nuclear transcription measurements of a representative rp-mRNA (L32 mRNA) revealed that following differentiation, its rate of synthesis relative to the overall transcription rate dropped by approximately 26% in myotubes while the rate of transcription of rRNA dropped by approximately 77%. These results indicate that the coordination of r-protein and rRNA synthesis observed in myoblasts was uncoupled in myotubes at the level of transcription.

Decrease in ribosomal proteins 1, 2/3, L4, and L7 in Drosophila melanogaster in the absence of X rDNA

The rRNA genes (rDNA) in Drosophila melanogaster are found in two clusters, one on the X and one on the Y chromosome. We have compared the ribosomal protein composition of wild-type Oregon-R flies containing both X-linked and Y-linked rDNA with that of flies containing only the Y-linked rDNA by two-dimensional polyacrylamide gel electrophoresis. Four basic proteins (1, 2/3, L4, and L7) normally present in wild-type flies were either electrophoretically not detectable (1, 2/3, and L4) or marginally detectable (L7) in flies with only Y-linked rDNA. No additional proteins were observed in these flies. However, immunodiffusion assays using specific antibodies raised against purified protein L4 confirmed that L4 was present but in relatively lower amounts in these Y-linked rDNA flies. An investigation was carried out to determine whether these electrophoretically undetectable proteins were more readily lost during ribosome preparation and hence were not readily detectable in the 80S particles by gel electrophoresis or whether they had been modified. Thus the proteins in the post-ribosomal cell supernatant and the high salt sucrose gradient were analyzed by two-dimensional gel electrophoresis and immunochemical assays with antibodies raised against protein L4 and total 80S ribosomal proteins. The experimental evidence indicates that there is a small amount of protein L4 and probably proteins 1, 2/3, and L7 in flies with only Y-linked rDNA but significantly less of these proteins than in wild-type flies.

A comparison of the ribosomal proteins of Drosophila ovary, adult, and embryo

The proteins in the 80S ribosomes of Drosophila melanogaster ovaries and adults have been characterized by two-dimensional polyacrylamide gel electrophoresis. When ribosomal proteins of ovaries and adults were compared with those from embryos, all 3 tissues showed a similar number of proteins. In addition, qualitatively, the electrophoretograms of proteins extracted from the ribosomes of these 3 tissues were found to be indistinguishable. However, apparent quantitative differences in certain acidic proteins were observed between tissues. Using ribosomes from embryos as a standard for comparison, ribosomes from adult flies that were more than 14 days old appeared to have relatively larger amounts of acidic proteins S7 and S9, and relatively smaller amounts of acidic proteins S14 and S25/S27. The transition period occurred during the ninth to thirteenth day of adult fly development. Significant differences were not detected between ovarian and embryonic acidic ribosomal proteins. In contrast to the differential ratio of acidic proteins in ovaries, adults, and embryos, a similar distribution of basic proteins was found in these tissues.

Comparative electrophoretic study on ribosomal proteins from algae

The proteins from cytoplasmic ribosomal subunits of eight species of algae were analyzed by two-dimensional gel electrophoresis. The molecular weights of the proteins were in the range of 10,000 to 55,000. We have compared the protein patterns from the ribosomal subunits of the different species to those of Chlamydomonas reinhardii. It was quite clear that there are many similarities in the protein patterns of all the investigated species. We found for Chlamydomonas eugametos 48, Chlamydomonas noctigama 42, Chlorogonium elongatum 47, Scenedesmus obliquus 40, Chlorella fusca 35, and Euglena gracilis 35 proteins which were homologous to those of Chlamydomonas reinhardii. For the colorless flagellate Polytoma papillatum, we detected 45 proteins homologous to Chlamydomonas reinhardii, so that the generally assumed close relationship between Chlamydomonas and Polytoma is confirmed.

Studies on ribosomal proteins in the cellular slime mold Dictyostelium discoideum. Resolution, nomenclature and molecular weights of proteins in the 40-S and 60-S ribosomal subunits

This study is concerned with the identification and subunit localization of ribosomal proteins in Dictyostelium discoideum. The characterization is based on the resolution of ribosomal proteins by various methods of electrophoresis. 34 and 42 unique proteins were identified in the 40-S and 60-S ribosomal subunits respectively. The total mass of proteins in the 40-S subunit was 746,100 daltons and 981,900 daltons in the 60-S subunit. The molecular weights of individual proteins in the 40-S subunit ranged from 13,200 to 40,900 with a number-average molecular weight of 21,900. The molecular weight range for the 60-S subunit was 13,800--51,100 with a number-average molecular weight of 23,400. The 80-S ribosome contained 78 proteins, two of which were lost upon its dissociation into subunits. All the proteins of the 40-S and 60-S subunits could be identified individually in a 80-S map as well as in unfractionated proteins from whole cells. Purification of ribosomes in high-ionic-strength buffers resulted in non-specific loss of the various proteins from the 40-S and 60-S subunits. In addition, the undissociated ribosomes contained about 10 acidic proteins in the molecular weight range 50,000--100,000, which were retained after washing the ribosomes in high-salt buffers. They were found in polysomes, run-off ribosomes and could also be identified in the 40-S subunit after dissociation.

Ribosomal protein modifications in liver injury: effect of carbon tetrachloride and extrahepatic cholestasis on protein phosphorylation

The phosphorylation of ribosomal proteins in rat liver injured fro various times by carbon tetrachloride and extrahepatic cholestasis was studied. The incorporation of [32P]phosphate into the protein moiety of the small ribosomal subunit was increased over 2-fold 1 to 4 h after injection of the hepatotoxin, whereas the specific activity of the 60 S subunit was low and changed only insignificantly. Two-dimensional electrophoretic analysis of ribosomal proteins complemented by autoradiography revealed that CCl4 stimulated the phosphorylation of only a single protein (S6) in the 40 S subunit. The phosphorylation of S6 led to a measurable anodic shift and elongation of the protein on the 2-dimensional electropherograms. In response to bile duct ligation a similar increase in phosphorylation of protein S6 was noticed.

Identification of neighbouring protein pairs in the rat liver 40-S ribosomal subunits cross-linked with dimethyl suberimidate

(1) The 40-S ribosomal subunits of rat liver were treated with a bifunctional cross-linking reagent, dimethyl suberimidate. Cross-linked protein-protein dimers were separated by two-dimensional acrylamide gel electrophoresis. The stained cross-linked complexes within the gel were radioiodinated without the elution of proteins from the gel and were cloven into the original monomeric protein constituents by ammonolysis. The proteins in each dimer were finally identified by two-dimensional acrylamide gel electrophoresis of the cloven monomeric proteins, followed by radioautography of the stained gel. (2) The molecular weights of cross-linked complexes were determined by SDS-polyacrylamide gel electrophoresis and were compared with those of their constituent proteins. (3) The following dimers were proposed from these results: S3-S12 (S3 or S3a-S11), S4-S12 (S3b-S11, S5-S7 (S4-S6), S5-S22 (S4-S23 or S24), S6-S8 (S5-S7), S8-S16 (S7-S18), S17-S21 (S16--S19) and S22A-S22B (S23-S24), designated according to our numbering system [1]. The designations according to the proposed uniform nomenclature [2] are described in parentheses.

Ribosomal proteins of the dimorphic fungus, Mucor racemosus

Ribosomal proteins of the dimorphic fungus Mucor racemosus were isolated and characterized by 2-dimensional gel electrophoresis. Proteins from ribosomes of the yeast and mycelial phase were compared, and were found to be qualitatively indistinguishable. The only consistent difference in the patterns of proteins was in a protein of the 40S subunit, S-6. This protein was phosphorylated in yeast and hyphae forms, but not in asexual sporangiospores. Studies on protein S-6 showed that it contained 3 phosphate residues per molecule of protein when maximally phosphorylated. In this form 3 different tryptic peptides were shown to contain a single phosphoserine. The S-6 protein also existed in forms containing 1 or 2 phosphates per molecule, depending on growth conditions.

Disulfide interaction in situ between two neighbouring proteins in mammalian 60-S ribosomal subunits. Isolation of the contact region of the larger protein

A disulfide complex is formed in situ under gentle conditions between two neighbouring proteins in the 60-S subunits of mammalian ribosomes. The proteins have been identified as L 4 and L 29. The complex is easily isolated from whole ribosomes, and can be utilized for preparing the two proteins in a very pure state for further characterization. Chymotryptic cleavage of the complex or the isolated larger protein (L 4) in the presence of SDS produces two unequal fragments of this protein in nearly quantitative yield. The smaller fragment (approx. 12 000 daltons) contains the contact sequence. Only this fragment of protein L 4 is labelled when rat liver ribosomes are incuabted with iodo[14C]acetate under conditions of complex formation. Protein L 29 is resistant to chymotrypsin in the presence of sodium dodecyl sulfate.

Ribosomes of Physarum polycephalum. Subunits and protein composition

Ribosomes from Physarum polycephalum were purified. Optimal conditions for preparation and stability of subunits were determined. KCl concentration above 200 mM induced protein dissociation from the subunits. It was observed that dissociated ribosomes were more stable in a low ionic strength buffer than in 200 mM KCl, where the 40 S was preferentially degraded by ribonucleases. Ribosomal proteins were analyzed by two-dimensional gel electrophoresis. The first dimension was carried out at pH 8.6 while the second was run at pH 4.6. The monosome contained sixty seven proteins, of which six were acidic. Two proteins were lost after subunit dissociation. Twenty six basic and two acidic proteins were observed in the 40 S subunit while the largest subunit gave thirty nine spots on the basic part of the gel and three additional spots on the acidic side. Five proteins were shared by 40 S and 60 S.

Spot position of rat liver ribosomal proteins by four different two-dimensional electrophoreses in polyacrylamide gel

Separation of the proteins from rat liver 40S and 60S ribosomal subunits and polysomes was done in four different two-dimensional polyacrylamide gel electrophoresis systems. The first dimension was run at acidic or basic pH, the second dimension either with sodium dodecyl sulphate or at acidic pH in 18% acrylamide. The position of each individual protein of both subunits and polysomes was determined in each system. This identification resulted from a new method avoiding any pervious purification of individual proteins. The new "proposed uniform nomenclature for mammalian ribosomal proteins" (McConkey et al. in press) was used for numbering the proteins in the four systems.

Ribosomal proteins in growing and starved Tetrahymena pyriformis. Starvation-induced phosphorylation of ribosomal proteins

The complements of ribosomal proteins in growing and starved cells of Tetrahymena pyriformis strain GL were examined by two-dimensional gel electrophoresis. In growing cells, the 40-S ribosomal subunit contained 30 proteins, 4 of which migrated toward the anode at pH 8.6, while the 60-S ribosomal subunit contained 46 proteins, 9 of which migrated toward the anode at pH 8.6. When exponentially growing cells were transferred into a non-nutrient medium pronounced phosphorylation of a single 40-S ribosomal subunit protein, S6, was induced. The phosphorylation was very specific; more than 99.5% of the [32P]phosphate incorporated into ribosomal proteins was associated with S6. Phosphate was incorporated into S6 as O-phosphoserine and O-phosphothreonine. Two-dimensional gel electrophoresis indicated that the complement of proteins associated with the ribosomes isolated from starved cells differed from that of growing cells. Careful examination, however, suggested that except for the phosphorylation of certain ribosomal proteins in starved cells, the observed differences did not reflect starvation-induced changes in vivo, but most probably different levels of artifactual modifications (limited proteolysis) during the preparation of the ribosomes.

Isolation and characterization of the acidic phosphoproteins of 60-S ribosomes from Artemia salina and rat liver

Eucaryotic L7/L12-type proteins are present in ethanol/salt extracts (P1 protein) of ribosomes from Artemia salina and rat liver. These proteins are partially phosphorylated and occur in two forms of closely related structure: a major form eL12 having methionine at the N-terminal position and a minor form of eL12 (eL12') which seems slightly elongated and contains a blocked N terminus. Purification of the four different forms of this protein, eL12, eL12-P, eL12' and eL12'-P, was performed by ion-exchange chromatography on carboxymethyl-cellulose and DEAE-cellulose. Using a radioimmuno assay, 1.8 copies of eL12 and 0.9 of eL12' were found on the 80-S A. salina ribosome. In ribosomes of both rat liver and A. salina, eL12 is present in a larger quantity than eL12'. 40-S and 60-S ribosomal subunits extracted with ethanol/salt were essentially free of eL12 proteins. A large pool of eL12 was found in the cytosol after removal of the ribosomes by centrifugation or molecular sieving. The proteins of rat liver and A. salina are similar with regard to their isoelectric points and molecular weights. Sedimentation equilibrium studies indicated that the isolated protein eL12 occurs as a dimer.

Ribosomal subunits from Tetrahymena pyriformis. Isolation and properties of active 40-S and 60-S subunits

Tetrahymena pyriformis ribosomal subunits were obtained by incubation of post-mitochondrial supernatant in the presence of 0.2 mM GTP and 0.1 mM puromycin for 45 min at 28 degrees C, followed by sucrose density gradient centrifugation. Isolated 40-S subunits were able to reassociate in vitro in the presence of 5 mM MgCl2 and 50 mM KCl and to perform poly(U)-dependent protein synthesis. The 60-S subunit carries the peptidyl transferase activity. The number of proteins in T. pyriformis ribosomal subunits was determined by two-dimensional polyacrylamide gel electrophoresis. The 40-S subunit contains 30 different protein species (including two acidic proteins). The 60-S subunit contains 35 different protein species (including two acidic proteins). The proteins were numbered following the system of Kaltschmidt and Wittmann.

Number and molecular weights of the basic proteins of rat liver ribosomes

1) Efficient separation of the proteins from rat liver ribosomes can by achieved by two-dimensional polyacrylamide gel electrophoresis. Complete separation of all components, however, is not possible with one system only. Comparison of the results obtained with different systems suggests further heterogeneity of S15, L22, L28, L33 and L35 and enables identification of S15a, S15b, L22a, L22b, L28a, L28b, L33, L33a, L35a and L36b. 2) Ribosomal proteins were substituted with iodoacetamide prior to electrophoresis or handled in all steps of the procedure in the presence of reducing agents. These procedures prevent the formation of oxidation products described erroneously as ribosomal proteins S5, S6, L15, L17 and L32 in earlier papers. 3) Estimation of the molecular weights was performed by two-dimensional separation of the small and large subunit proteins using sodium dodecyl sulphate in the second dimension. The positions of the 70 basic proteins in the 2-D patterns were identified. 4) The small and large subunit proteins have molecular weights in the range of 8000 to 35,000 and 11,000 to 55,500 Dalton, respectively. The number average molecular weights for the small and large subunit proteins are 22,500 and 26,500 Dalton, respectively. The sum of the molecular weights is 0.67 x 10(6) Dalton for the proteins of the small subunit and 1.05 x 10(6) Dalton for the proteins of the large subunit.

Characterization of the acidic phosphorprotein of eukaryotic ribosomes using a new system of two-dimensional gel-electrophoresis

1. A modified method of two-dimensional gel electrophoresis has been developed for detecting acidic eukaryotic ribosomal proteins. 2. Using this method it has been demonstrated that the major phosphoprotein (Lgamma) of mouse ascites and hamster fibroblast 60-S ribosomal subunits is an acidic protein, apparently analagous to L7/12 of Escherichia coli, and not a neutral protein as previously thought. Electrophoretic resolution of phosphorylated and non-phosphorylated forms of Lgamma has enabled the stoichiometric nature of the phosphorylation (previously deduced from measurement of the specific radioactivity of the ATP pool) to be confirmed. 3. When ascites cells were incubated for 3 h there appeared an altered form of Lgamma which is most likely produced by proteolytic cleavage of the original form. The extent of phosphorylation of Lgamma was decreased by one-half or more in these circumstances. 4. Phosphoprotein Lgamma was found to be almost completely phosphorylated in both polyribosomes and monoribosomes isolated from hamster fibroblasts. Thus the function of the phosphorylation of Lgamma appears not to be concerned with the inactivation of ribosomes.

Characterisation of ribosomal proteins from HeLa and Krebs II mouse ascites tumor cells by different two-dimensional polyacrylamide gel electrophoresis techniques

Electrophoresis of ribosomal proteins according to Kaltschmidt and Wittmann, 1970a, b (pH 8.6/pH 4.5 urea system) yielded 29 proteins for the small subunits and 35 and 37 proteins for the large subunits of Krebs II ascites and HeLa ribosomes, respectively. Analysis of the proteins according to a modified technique by Mets and Bogorad (1974) (pH 4.5/pH 8.6 SDS system) revealed 28 and 29 proteins in the small subunits and 37 and 38 proteins in the large subunits of Krebs II ascites and HeLa ribosomes. The molecular weights of the individual proteins were determined by: 1. "three-dimensional" gel electrophoresis; 2. two-dimensional gel electrophoresis at pH 4.K/pH 8.6 in SDS. The molecular weights for 40S proteins ranged from 10,000 to 39,000 dalton (number average molecular weight: 21,000). The molecular weights for the 60S proteins ranged from 14,000 to 44,000 dalton (number average molecular weight: 23,000) using the "three-dimensional" technique. A molecular weight range from 10,000 to 38,000 dalton (number average molecular weight: 21,000) was obtained for the 40S subunits, whereas the molecular weights for the 60S ribosomal proteins (average molecular weight: 26,000) ranged from 12,000 to 69,000 dalton using the pH 4.5/pH 8.6 SDS system. The molecular weights Krebs II ascites and HeLa ribosomal proteins are compared with those obtained by other authors for different mammalian species.

Characterization of proteins from nucleolar preribosomes of mouse leukemia cells by two-dimensional polyacrylamide gel electrophoresis

Proteins of isolated 80-S and 60-S nucleolar preribosomal particles were characterized by means of two-dimensional polyacrylamide gel electrophoresis, in the lymphocytic mouse leukemia cells L5178Y. Their identification and metabolic relationships with ribosomal subunit proteins were investigated using co-electrophoresis of unlabeled polysomal proteins with labeled proteins of either nucleolar preribosomes or ribosomal subunits. The large and small ribosomal subunits contain 40 and 31 proteins, respectively. The nucleolar 80-S preribosomes were analysed after 2 and 5 h of incubation with tritiated valine and leucine and were shown to contain about 55 proteins. Most of them were identical to cytoplasmic ribosomal subunit proteins. The nucleolar 60-S preribosomes contain all the proteins which are common to 80-S preribosomes and large ribosomal subunits, and one additional protein (L10). The ribosomal proteins which were absent from nucleolar particles were found to be labeled in the cytoplasmic ribosomes after the same incubation period. Thus, in addition to the association of the bulk of ribosomal proteins with 45-S RNA within the 80-S preribosomes, results indicate that a group of ribosomal proteins and particularly from the small subunits, become associated at later stages of the maturation process of mammalian ribosomes. It was further shown that a set of 10 proteins, different from ribosomal polypeptides, were present in nucleolar preribosomal particles. Several of them were associated with polyribosomes in the cytoplasm, whereas the others were unique to the nucleolus.

Phosphorylation in vivo of Ribosomes in Tetrahymena pyriformis

Phosphorylation of ribosomal proteins in vivo was studied in exponentially growing and starved cells of the ciliated protozoan, Tetrahymena pyriformis. No phosphorylation of ribosomal proteins could be demonstrated in cells growing exponentially in complex nutrient media. However, when Tetrahymena cells were transferred into a non-nutrient medium, pronounced phosphorylation of a single ribosomal protein was observed. During two-dimensional polyacrylamide gel electrophoresis the phosphorylated ribosomal protein migrated in a manner virtually identical to that of the phosphorylated ribosomal protein S6 of rat liver. The phosphorylated ribosomal protein has a molecular weight of 38000 as estimated by dodecylsulfate polyacrylamide gel electrophoresis. Thus, the phosphorylated ribosomal protein found in starved Tetrahymena is apparently homologous with the ribosomal protein which is predominantly phosphorylated in higher eukaryotes. When phosphorylated ribosomes were dissociated by treatment with high concentration of KCl, the phosphorylated protein was found only on the small subunit. If dissociation was achieved by dialysis against a buffer low in MgCl2, the phosphorylated protein was distributed almost equally between the two subunits. This indicates that the phosphorylated ribosomal protein is located at the interface between the two subunits.

Ribosomal proteins of HeLa cells

Ribosomal proteins from HeLa cells were analyzed by two-dimensional polyacrylamide gel electrophoresis (Kaltschmidt-Wittmann) and dodecylsulfate polyacrylamide gel electrophoresis (Laemmli). 35 proteins are associated with the small ribosomal subunit and 47 proteins with the large ribosomal subunit. The HeLa ribosomal proteins S6, S32, L40b,c, L41 and L42 are phosphorylated in vivo and in vitro. Minor differences between HeLa and rat liver ribosomal proteins were revealed by their direct coelectrophoresis.

Quantitative variation of a 60S ribosomal protein during growth of the fungus Podospora anserina

During the growth phase, in the fungus Podospora anserina, a variation is observed in the composition of the ribosomal proteins. A protein of the 60S subunit which is absent in the ribosomes from 2 days old cultures becomes gradully more abundant as the culture time is prolonged.

Ribosomal proteins in the fungus Podospora anserina: evidence for an electrophoretically altered 60S protein in a cycloheximide resistant mutant

Proteins of cytoplasmic ribosomes of the Podospora anserina were analyzed by two dimensional gel electrophoresis. The numbers of proteins were estimated to be 28 in the small subunit and 41 in the large subunit. The L21 protein of the large subunit was found to migrate differently in a cycloheximide resistant mutant.

Ribosomal proteins of mouse kidney: normal status and during compensatory renal hypertrophy

Ribosomes were isolated from normal and growing kidney and the protein complement was examined by a two-dimensional gel electrophoretic procedure. Proteins were resolved in the first dimension on the basis of charge and, in the second dimension, on the basis of molecular weight. 60S and 40S ribosomal subunits from normal kidney contained respectively 42 and 31 proteins. 80S ribosomes contained 23 proteins not found with either sub-unit. Nineteen of these proteins were removed from the ribosomes when isolated ribosomes were washed in a high salt buffer. Six proteins of the 80S ribosome corresponded to proteins associated with both sub-units. 80S ribosomal proteins were also studied during compensatory renal hypertrophy after 4-96 h of induced growth. The protein complement displayed by electrophoresis was identical to the pattern seen from normal renal cells.

In vivo incorporation of ribosomal proteins into HeLa cell ribosomal particles

Using high salt-washed ribosomal subunits from HeLa cells we detect three ribosomal proteins from the small subunit and five ribosomal proteins from the large subunit that enter ribosomal particles in the absence of ribosome formation (actinomycin D-treated cells); in untreated cells, they enter the ribosomal particles quickly, while the rest of the ribosomal proteins are incorporated gradually. At least two of the large subunit actinomycin D-resistant ribosomal proteins seem to be absent in the 55 S nucleolar ribosomal precursor.

Iodination-deiodination. A radiochemical method for detection of structure and changes in structure in RNA

Bound iodine is released from radioiodinated nucleotides in polymers exposed to sodium bisulfite. The rate of bisulfite-catalyzed deiodination of pyrimidines can be controlled both by change of temperature of pH and is also dependent on the molecular association of the nucleotide. The rate of release of iodine from iodocytidine in polycytidylate is greater than the rate of elimination from RNA. Experiments testing the influence of base-pairing of the iodopyrimidines in synthetic polynucleotides showed that pairing of the substituted nucleotide protected the iodine bond. The rates of bisulfite-catalyzed deiodination of several radioiodinated RNAs were measured. The action of bisulfite on all single stranded RNAs tested was multiphasic consisting of a rapid early deiodination reaction supplanted by a slower phase which was followed by reacceleration of release. The release of iodine from double stranded RNA and DNA-RNA duplexes was retarded in comparison with the release from ribosomal and messenger RNA fractions. The deiodination profiles of single and double stranded RNA suggested that the intermediate stage iodine release is governed by melting of paired zones of low stability. Late release may result from destablization of the molecule through the addition of bisulfite to the pyrimidine ring or deamination. The effect of several substances expected to complex with polynucleotides was tested. Acridine orange and ethidium bromide increased loss of iodine from ribosomal RNA but slightly decreased elimination from double stranded viral RNA. A basic protein fraction isolated from ribosomal particles accelerated the deiodination of ribosomal RNA. While the destabilization caused by this protein fraction was greater than that caused by an equal amount of albumin, as tested the effect was non-specific. The results show that a change in sensitivity to chemical deiodination may folow the interaction of small amounts of protein with polynucleotides.