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

Metabolite sensing and signaling in cell metabolism

Metabolite sensing is one of the most fundamental biological processes. During evolution, multilayered mechanisms developed to sense fluctuations in a wide spectrum of metabolites, including nutrients, to coordinate cellular metabolism and biological networks. To date, AMPK and mTOR signaling are among the best-understood metabolite-sensing and signaling pathways. Here, we propose a sensor-transducer-effector model to describe known mechanisms of metabolite sensing and signaling. We define a metabolite sensor by its specificity, dynamicity, and functionality. We group the actions of metabolite sensing into three different modes: metabolite sensor-mediated signaling, metabolite-sensing module, and sensing by conjugating. With these modes of action, we provide a systematic view of how cells sense sugars, lipids, amino acids, and metabolic intermediates. In the future perspective, we suggest a systematic screen of metabolite-sensing macromolecules, high-throughput discovery of biomacromolecule-metabolite interactomes, and functional metabolomics to advance our knowledge of metabolite sensing and signaling. Most importantly, targeting metabolite sensing holds great promise in therapeutic intervention of metabolic diseases and in improving healthy aging.

A simple, three-part model provides a systematic view of how cells sense sugars, lipids, amino acids and metabolic intermediates. Cells quickly and accurately perceive changes in intra- and extracellular molecules such as nutrients to respond to changing environments. Drawing on existing knowledge about AMPK and MTORC1 signaling, Yi-Ping Wang and Qun-Ying Lei at Fudan University in Shanghai propose a model in which three components: a sensor, transducer and effector enable metabolic sensing and signaling to proceed. The sensor detects the metabolite, and, through conjugation, conformational changes or protein–protein interactions, transmits this information to the transducer, which decides the appropriate response. The transducer then issues orders to effector proteins which coordinate the action. The future identification of novel metabolic sensors through systematic screening could lead to new therapeutic interventions for metabolic and age-related diseases.

Regulation of synthesis of cell-specific ribosomal proteins during differentiation of Dictyostelium discoideum

Proteins of ribosomes from various stages of development in Dictyostelium discoideum were analyzed by two-dimensional polyacrylamide gel electrophoresis. Significant changes in protein composition were observed; the data demonstrate that cell differentiation in a eukaryotic system is accompanied by ribosome heterogeneity. Both qualitative and quantitative differences were noted for 12 unique ribosomal proteins between the vegetative amoebae and spores (differentiated cells). Two proteins were specific to ribosomes of amoebae, and three were specific to spores. The others were common to both cells but showed characteristic stoichiometric changes. The appearance and quantitative changes of these proteins were associated with specific stages of cell differentiation and were evident only during the aggregation phase; however, further changes continued through construction of fruiting bodies. As functional mRNAs for all 12 proteins were present in both amoebae and spores, both transcriptional and translational mechanisms apparently regulate the synthesis of the various developmentally controlled ribosomal proteins in the two cell types.

Monovalent cation-dependent reversible phosphorylation of ribosomal protein S8 in growth arrested Tetrahymena: kinetics of formation, phosphoamino acids, and phosphopeptides of mono-, and diphosphorylated derivatives of protein S8

The kinetics of formation of mono-, and diphosphorylated derivatives of ribosomal protein S8 in Tetrahymena starving in the presence of Na+ have been determined, and the phosphoamino acids present in these derivatives have been identified. The mono-phosphorylated product, S8', contains only phosphoserine, and behaves kinetically as the precursor of the diphosphorylated product S8" which contains phosphoserine, and phosphothreonine. Tryptic digestion release a single major phosphoserine containing peptide from both S8' and S8", and a single phosphothreonine containing peptide from S8".

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.

Phosphorylation of the Saccharomyces cerevisiae equivalent of ribosomal protein S6 has no detectable effect on growth

The phosphorylation of mammalian ribosomal protein S6 is affected by a variety of agents, including growth factors and tumor promoters, as well as by expressed oncogenes. Its potential role in the regulation of protein synthesis has been the object of much study. We have developed strains of Saccharomyces cerevisiae in which the phosphorylatable serines of the equivalent ribosomal protein (S10) were converted to alanines by site-directed mutagenesis. The S10 of such cells is not phosphorylated. Comparison of these cells with the parental cells, whose genomes differ by only six nucleotides, revealed no differences in the lag phase or logarithmic phase of a growth cycle, in growth on different carbon sources, in sporulation, or in sensitivity to heat shock. We conclude that in S. cerevisiae the phosphorylation of ribosomal protein S10 may play no role in regulating the synthesis of proteins. This conclusion leads one to ask whether certain protein phosphorylations are simply the adventitious, if easily observable, result of the imperfect specificity of one or another protein kinase.

Phosphorylation of the Saccharomyces cerevisiae equivalent of ribosomal protein S6 has no detectable effect on growth

The phosphorylation of mammalian ribosomal protein S6 is affected by a variety of agents, including growth factors and tumor promoters, as well as by expressed oncogenes. Its potential role in the regulation of protein synthesis has been the object of much study. We have developed strains of Saccharomyces cerevisiae in which the phosphorylatable serines of the equivalent ribosomal protein (S10) were converted to alanines by site-directed mutagenesis. The S10 of such cells is not phosphorylated. Comparison of these cells with the parental cells, whose genomes differ by only six nucleotides, revealed no differences in the lag phase or logarithmic phase of a growth cycle, in growth on different carbon sources, in sporulation, or in sensitivity to heat shock. We conclude that in S. cerevisiae the phosphorylation of ribosomal protein S10 may play no role in regulating the synthesis of proteins. This conclusion leads one to ask whether certain protein phosphorylations are simply the adventitious, if easily observable, result of the imperfect specificity of one or another protein kinase.

Phosphorylation of a 40S ribosomal subunit protein in Tetrahymena. Lack of correlation with cellular growth and ribosome stability

In Tetrahymena the small ribosomal subunit protein S7, which appears to be the equivalent of S6 of higher eukaryotes, undergoes reversible phosphorylation under a set of defined conditions. In an attempt to understand the physiological role of such reversible phosphorylation, we examined the status of ribosomal protein S7 in growing cells and growth-arrested cells, starving either non-specifically for nutrients or specifically for a single essential amino acid. These experiments allowed us to dissociate S7 phosphorylation from changes in the translational activity and the stability of ribosomes. The results revealed complete lack of correlation between phosphorylation of S7 and both the growth status of the cells and the in vivo stability of ribosomes. Taken together with the observation that phosphorylation of S7 occurs only when the cells are starved in buffers containing sodium chloride or high concentrations of Tris, non-essential ions for normal growth, our data suggest that this protein modification is required to maintain the functional integrity of the ribosomes in an altered electrostatic environment, induced by changes in the extracellular ionic conditions.

Immunological homologies between ribosomal proteins amongst lower eukaryotes

Polyclonal antibodies were raised against the purified ribosomal proteins L1 and L2, the 5S rRNA binding protein L3, all from Saccharomyces cerevisiae, and against L1 and L2 from Schizosaccharomyces pombe (numbering according to Otaka and Osawa 1981; Otaka et al. 1983, respectively). For clarity prefixes Sc and Sp have been added to the numbering of proteins derived from S. cerevisiae and S. pombe, respectively. Ribosomal proteins from these yeasts and from Kluyveromyces marxianus, Rhodotorula glutinis, the slime mold Dictyostelium discoideum and the protozoan Tetrahymena thermophila were checked for antigenic cross-reactivity by the immunoblot technique. Anti-ScL1 bound to the largest ribosomal proteins of all organisms but not with equal strength. A fast migrating protein band from R. glutinis was also reactive. Anti-ScL2 reacted strongly with L2 or analogous proteins derived exclusively from the yeasts. Anti-ScL3 cross-reacted only with one protein band from K. marxianus, whereas anti-SpL1 cross-reacted with L1 or its analogues from the other organisms, but also with proteins of lower molecular weight. In S. cerevisiae, these proteins are located exclusively on the small ribosomal subunit. L2 or analogous ribosomal proteins of all organisms were recognized by anti-SpL2 but additionally the ribosomal protein YL28 of S. cerevisiae and fast migrating proteins of T. thermophila exhibited anti-SpL2 binding.

The specific phosphorylation of a 40S ribosomal protein in growth-arrested tetrahymena is induced by sodium

In the past few years, in vivo phosphorylation of ribosomal proteins has been the subject of extensive studies and the results have shown that reversible phosphorylation of small subunit ribosomal protein S6, ubiquitous in eukaryotic cells, is apparently related to regulation of protein synthesis initiation. Thus the level of protein synthesis under various conditions is correlated with the level of S6 phosphorylation. In exponentially growing Tetrahymena, however, such phosphorylation does not occur, but when these cells are transferred to starvation buffers, the rate of protein synthesis is drastically reduced and a 40S ribosomal protein analogous to S6 of higher eukaryotic cells is fully and rapidly phosphorylated in all the ribosomes. We have studied the conditions which lead to this phosphorylation in growth-arrested Tetrahymena, in order to understand the physiological significance of this process. Our results show that there is no obvious correlation between this phosphorylation and starvation. Moreover, it is not a developmentally regulated process related to the conjugation cycle, but a modification induced by the presence of sodium ions or high concentration of Tris in the starvation buffer. The physiological significance of this process is discussed in terms of accumulation of negative charge density probably required for initiation of protein synthesis in the growth-arrested cells starving in Na+-containing buffers.

Regulation of ribosome synthesis in Tetrahymena pyriformis. 1. Coordination of synthesis of ribosomal proteins and ribosomal RNA during nutritional shift-down

When exponentially growing cells of Tetrahymena pyriformis are transferred to a non-nutrient medium the loss of whole cell RNA, 90% of which is ribosomal RNA, exhibits biphasic kinetics, whereas whole cell protein is lost at a constant rate. The ratio RNA/protein declines during the first 5 h of starvation and then remains constant during the subsequent period of starvation. The synthesis of the majority of the ribosomal proteins is coordinately regulated during a nutritional shift-down. Exponentially growing cells devote 17% of their capacity for protein synthesis to the production of ribosomal proteins. Upon starvation this proportion is rapidly reduced 3.5-fold. In long-time-starved cells the absolute rate of ribosomal protein synthesis is only about 4.5% of that of exponentially growing cells. The synthesis of ribosomal RNA and ribosomal proteins appears tightly coupled during the transition from growth to starvation. In long-time-starved cells the synthesis of ribosomal RNA and ribosomal proteins are stoichiometrically balanced with no significant degradation of de novo synthesized ribosomal proteins.

Ribosomal subunits and ribosomal proteins of Tetrahymena thermophila. Effect of the presence of iodoacetamide during ribosome extraction on the properties of the subunits

Proteolytic degradation of ribosomal proteins occurs during the preparation of subunits of the cytoplasmic ribosomes of the protozoa Tetrahymena thermophila and the isolated subunits are inactive. Addition of 5 mM iodoacetamide to cell suspensions before extraction inhibits proteolytic activity and permits isolation of active subunits. The protein complements of these subunits have been characterized in two different two-dimensional electrophoretic systems, and their molecular weights have been determined.

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.

Phosphorylation of ribosomal proteins S3, L1 and L24 during spherulation in Physarum polycephalum

The phosphate content of ribosomal proteins S3, L1 and L24 has been determined in the course of spherulation of Physarum polycephalum. The major phosphoprotein, S3, was completely dephosphorylated after 4 h of differentiation. The phosphate content of L1 and L24 was not altered during the differentiation. The cellular level of ATP remained constant for at least 5 h. A 3-fold reduction of cyclic AMP concentration occurred in the first hour, followed by a slow increase to a final value of twice the level observed in growing cells. The results showed that the phosphorylation of ribosomal proteins is regulated by at least two different mechanisms and that the dephosphorylation of S3 is not induced by a lack of cellular ATP. Although cyclic AMP might trigger the dephosphorylation of S3, the phosphate content of this protein remained at a very low value even when the cellular concentration of cyclic AMP rose significantly. Since the polysome level remains constant during the first 24 h of spherulation, the phosphorylation of S3 is not necessary for active protein synthesis and the phosphorylation of L1 and L24 is not involved in ribosome inactivation, which occurs after 24 h.

Turnover rates of phosphoryl groups in ribosomal proteins of Physarum polycephalum. Evidence for two different mechanisms

The rate of phosphate exchange in individual ribosomal proteins of Physarum polycephalum was determined in vivo. It was observed that the phosphoryl groups of S3, the major phosphoprotein, had a turnover rate of 1.5% per minute. The phosphoryl groups of proteins L1, L20 and L24 were stable. These results show that the phosphorylation of ribosomal proteins is regulated by at least two different mechanisms. The rapid turnover of phosphoryl groups of the major phosphoprotein is in agreement with the general observation that the phosphate content of this protein is modulated by the physiological state of the cells and possibly involved in the regulation of ribosome activity. The absence of phosphate exchange in acidic proteins suggests that these groups could play a structural role in the ribosome functions.

Identification of homologous ribosomal proteins in HeLa cells and in Tetrahymena pyriformis. A study of proteins binding 5-S RNA and acidic proteins released from 40-S subunits by EDTA

Tetrahymena pyriformis 60-S ribosomal subunits treated with EDTA release a 7-S particle containing 5-S RNA and a 36000-Mr protein that is similar to mammalian 5-S-RNA-binding protein L5 in molecular weight, in two-dimensional acrylamide gel mobility, and in peptide pattern as generated by a simple, one-dimensional acrylamide gel technique. Human and T. pyriformis 40-S ribosomal subunits, treated with buffers lacking magnesium or containing EDTA, release varying amounts of two large acidic proteins. We have identified these released proteins by two-dimensional gel electrophoresis.