Comparison of the protein content of free and membrane-bound rat liver polysomes and of the derived subunits

Purification of ribosomes from human cell lines

Highly conserved during evolution, the ribosome is the central effector of protein synthesis. In mammalian cells, the ribosome is a macromolecular complex composed of four different ribosomal RNAs (rRNA) and about 80 ribosomal proteins. Requiring more than 200 factors, ribosome biogenesis is a highly complex process that takes place mainly within the nucleoli of eukaryotic cells. Crystallographic data suggest that the ribosome is a ribozyme, in which the rRNA catalyses the peptide bond formation and ensures quality control of the translation. Ribosomal proteins are involved in this molecular mechanism; nonetheless, their role is still not fully characterized. Recent studies suggest that ribosomes themselves and/or the mechanisms underlying their synthesis, processing, and assembly play a key role in the establishment and progression of several human pathologies. The protocol described here is simple, efficient, and robust, and allows one to purify high-quality ribosomes from human cultured cell lines. Ribosomes purified with this protocol are adequate for most of the subsequent analyses of their RNA and protein content.

Dysregulation of ribosome biogenesis and translational capacity is associated with tumor progression of human breast cancer cells

Protein synthesis is a fundamental cell process and ribosomes - particularly through the ribosomal RNA that display ribozyme activity - are the main effectors of this process. Ribosome biogenesis is a very complex process involving transcriptional as

well as many post-transcriptional steps to produce functional ribosomes. It is now well demonstrated that ribosome production is enhanced in cancer cells and that ribosome biogenesis plays a crucial role in tumor progression. However, at present there is an important lack of data to determine whether the entire process of ribosome biogenesis and ribosome assembly is modified during tumor progression and what could be the potential impact on the dysregulation of translational control that is observed in cancer cells. In breast cancer cells displaying enhanced aggressivity, both in vitro and in vivo, we have analyzed the major steps of ribosome biogenesis and the translational capacity of the resulting ribosome. We show that increased tumorigenicity was associated with modifications of nucleolar morphology and profound quantitative and qualitative alterations in ribosomal biogenesis and function. Specifically cells with enhanced tumor aggressivity displayed increased synthesis of 45S pre-rRNA, with activation of an alternative preRNA synthetic pathway containing a 43S precursor and enhanced post-transcriptional methylation of specifc sites located in the 28S rRNA. While the global translational activity was not modified, IRES-initiated translation, notably that of p53 mRNA, was less efficient and the control of translational fidelity was importantly reduced in cells with increased aggressivity. These results suggest that acquisition of enhanced tumor aggressivity can be associated with profound qualitative alterations in ribosomal control, leading to reduced quality control of translation in cancer cells

Increased calcium influx and ribosomal content correlate with resistance to endoplasmic reticulum stress-induced cell death in mutant leukemia cell lines

Cell clones were derived by treatment of HL-60 cells with stepwise increasing concentrations of econazole (Ec), an imidazole antifungal that blocks Ca2+ influx and induces endoplasmic reticulum (ER) stress-related cell death in multiple mammalian cell types. Clones exhibit 20- to more than 300-fold greater resistance to Ec. Unexpectedly, they also display stable cross-resistance to tunicamycin, thapsigargin, dithiothreitol, and cycloheximide but not doxorubicin, etoposide, or Fas ligand. Phenotypic analysis indicates that the cells display increased store-operated calcium influx and resistance to ER Ca2+ store depletion by Ec. E2R2, the most resistant clone, was observed to maintain protein synthesis levels after treatment with Ec or thapsigargin. Expression of GRP78, an ER-based chaperone, was induced by these ER stress treatments but to equal degrees in HL-60 and E2R2 cells. By using microarray analysis, at least 15 ribosomal protein genes were found to be overexpressed in E2R2 compared with HL-60 cells. We also found that ribosomal protein content was increased by 30% in E2R2 as well as other clones. The resistance phenotype was partially reversed by the ribosome-inactivating protein saporin. Therefore, increased store-operated calcium influx, resistance to ER Ca2+ store depletion, and overexpression of ribosomal proteins define a novel phenotype of ER stress-associated multidrug resistance.

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.

Protein synthesis directed by polyadenylated and non-polyadenylated RNA isolated from membrane-bound and free polysomes of Tetrahymena pyriformis

Free and membrane-bound polysomes were prepared from the protozoa Tetrahymena pyriformis using a procedure which gives good recovery and practically no cross-contamination. Polysomes are intact as analysed by sedimentation analysis. Poly(A)-rich RNA and poly(A)-free RNA, isolated from both populations of polysomes, show similar electrophoretic patterns. These RNAs were translated in the rabbit reticulocyte lysate cell-free system and the translation products were analysed by one-dimensional and two-dimensional gel electrophoresis. The most striking differences were found in the two-dimensional electrophoretic analysis namely: (a) a group of polypeptides (10) is synthesized mainly on membrane-bound polysomes, (b) a second abundant group is synthesized mainly in free polysomes (c) and a third class of polypeptides is synthesized on both kinds of polysomes. Poly(A)-free RNAs, isolated from free polysomes, are also able to promote synthesis of some polypeptides. The results are discussed taking into account the fact that T. pyriformis is a non-secretory cell.

Carbodiimide-induced protein--RNA crosslinking in mammalian ribosomal subunits

RNA--protein interactions in the 60 S subunits of rat liver ribosomes were studied using 1-ethyl-3-dimethylaminopropyl carbodiimide (EDC) under conditions which neither changed the sedimentation coefficient of subunits nor the intactness of their rRNA. EDC induced RNA--protein and protein--protein crosslinkings. Proteins crosslinked to 28 S RNA were identified by two-dimensional gel electrophoreses as L17, L19, L23a and L37a, shown to react with 28 S RNA when using a low dose of UV radiation. Attempts have also been made to use EDC for the studies of RNA--protein interactions in 40 S ribosomal subunits.

Photoincorporation of tetracycline into rat-liver ribosomes and subunits

[3H]Tetracycline was covalently incorporated into rat liver ribosomes and isolated 40-S and 60-S subunits on irradiation at 254 nm. The antibiotic was almost exclusively incorporated into ribosomal proteins. At least some of these proteins are assumed to be involved in ribosomal function, since photoincorporated tetracycline was found to inhibit the activity of 40-S and 60-S subunits in the poly(U)-directed protein-synthesizing system as well as that of the 40-S subunit in the poly(U)-mediated [14C]Phe-tRNA binding. The results from simultaneous one-dimensional and two-dimensional gel electrophoreses showed a small distribution of label among ribosomal proteins in 60-S subunits and in 80-S ribosomes, L10 being the most radioactive protein. As non-acylated tRNA partly competed with this labeling, it is likely that tetracycline interaction with these proteins occurred at a functional site. L10 has already been found to interact with puromycin [Reboud, A. M., Dubost, S., Buisson, M. & Reboud, J. P. (1981) Biochemistry, 20, 5281-5288]. In the case of feed 40-S subunits the label distribution was wider among ribosomal proteins. No particular role has yet been found for the most labeled protein, S12, but protein S3a, which was also highly labeled, has already been reported to be involved in subunit function.

Bombyx mori L. ribosomal proteins: resolution, nomenclature, molecular weights and in vivo phosphorylation

Bombyx mori L. ribosomal proteins have been analyzed by four related two-dimensional polyacrylamide gel electrophoretic systems (Madjar et al. 1977a). In the small and large subunits are present 32 and 45 proteins, respectively, whose numbering is proposed. No significant differences in composition or migration could be detected between proteins in membrane-bound ribosomes and free ribosomes. The molecular weights of the proteins vary from 60,000 to less than 10,000. In vivo phosphorylation was investigated by labeling with 32P-orthophosphate. Autoradiograms of four two dimensional gels unambiguously show five labeled ribosomal proteins: S1, S7, L6, L29, and L40.

Differences in electrophoretic behaviour of eight ribosomal proteins from rat and rabbit tissues and evidence for proteolytic action on liver proteins

Divergence exists between eight ribosomal proteins of rat and rabbit. This is the first time such a divergence has been precisely demonstrated among mammals. In addition, a proteolytic activity, giving the appearance of modified proteins, is observed in the liver of both species but not in rabbit reticulocytes. These results were made possible by a recently developed method. Ribosomal proteins were compared by two-dimensional polyacrylamide gel electrophoresis in four different but related systems. The precise position of each individual protein was established in each of the four systems. Certain ribosomal proteins from different tissues, seemingly identical in one system were found to be different in other systems. Significant differences occurred between proteins of each ribosomal subunit from the two different species. Variation between reticulocyte and liver ribosomal proteins of the rabbit were minor. Several liver proteins of both species change position or disappear and apparently new proteins appear, if appropriate steps are not taken to prevent proteolysis. Differences in behavior of three small subunit and five large subunit proteins are attributable to an evolutionary divergence between the two species.

Photo-induced protein-RNA cross-linking in mammalian 60-S ribosomal subunits

Rat liver 60-S ribosomal subunits were submitted to increasing doses of radiation (253.7 nm), at 4 degrees C and 25 degrees C, as previously reported fro 40-S subunits. The existence of protein-RNA cross-linking was demonstrated by two methods. The first consisted in the separation of protein-RNA complex; the second was indirect, and took into account alteration either in the electrophoretic mobility of cross-linked proteins or the separability of 28-S RNA in a 4 M urea/3 M LiCl buffer. The peptide synthetase activity and the sedimentation characteristics of the particles irradiated at 4 degrees C were well preserved, but at 25 degrees C the large subunits were progressively inactivated and unfolded for doses higher than 2 x 10(18) quanta. The dose-dependent variations of protein cross-linkage determined by two-dimensional gel electrophoresis allowed us to distinguish those proteins which reacted at the lowest doses with a first-order reaction from those which cross-linked to RNA after a subtle modification of the subunit structure. At 25 degrees C, all proteins became low-dose reactive. The curve obtained for 28-S RNA cross-linkage was similar to that of the total protein moiety, while those obtained fro the 5-S and 5.8-S RNA (which were parallel) suggest a lower reactivity of these RNAs. As a general rule, proteins from the large subunits were more reactive to RNA than those from the small subunits. This could indicate differences in the organisation of the two subunits.

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.

Photo-induced protein-RNA cross-linking in mammalian 40-S ribosomal subunits

RNA-protein interaction in the 40-S subunits of rat liver ribosomes were studied by measuring cross-linking of proteins to RNA induced by ultraviolet radiation. Under conditions which caused neither extensive degradation of the 40-S subunits (or 18-S RNA) nor biological inactivation, the total staining intensity of the proteins extracted from irradiated subunits was considerably reduced on the two-dimensional electrophoregrams. Convincing evidence was obtained that cross-linking of the proteins to 18-S RNA was the predominant reaction. The cross-linking extent of the individual proteins was studied as a function of the radiation dose. At 4 degree C, 13--15 proteins were found to cross-linked to RNA even at low doses of quanta. They generally correspond to proteins which have been previously shown to react poorly on the ribosomes with various chemical reagents. At 25 degree C, all the proteins became cross-linked to RNA using the same radiation doses.

Occurrence of phosphorylated forms of an acidic protein in the large ribosomal subunit of rat liver

An acidic protein from rat liver 60-S ribosomal subunits was selectively extracted with 50% ethanol. It was revealed as three different spots by two-dimensional gel electrophoresis, two of them being attributable to phosphorylated forms since they disappeared after alkaline phosphatase treatment. The relationship between this protein and similar acidic proteins found in eucaryotic cells is discussed.