Determination of the number of active muscle ribosomes: effect of diabetes and insulin

Diabetes risk loci-associated pathways are shared across metabolic tissues

Aims/hypothesis

Numerous genome-wide association studies have been performed to understand the influence of genetic variation on type 2 diabetes etiology. Many identified risk variants are located in non-coding and intergenic regions, which complicates understanding of how genes and their downstream pathways are influenced. An integrative data approach will help to understand the mechanism and consequences of identified risk variants.

Methods

In the current study we use our previously developed method CONQUER to overlap 403 type 2 diabetes risk variants with regulatory, expression and protein data to identify tissue-shared disease-relevant mechanisms.

Results

One SNP rs474513 was found to be an expression-, protein- and metabolite QTL. Rs474513 influenced LPA mRNA and protein levels in the pancreas and plasma, respectively. On the pathway level, in investigated tissues most SNPs linked to metabolism. However, in eleven of the twelve tissues investigated nine SNPs were linked to differential expression of the ribosome pathway. Furthermore, seven SNPs were linked to altered expression of genes linked to the immune system. Among them, rs601945 was found to influence multiple HLA genes, including HLA-DQA2, in all twelve tissues investigated.

Conclusion

Our results show that in addition to the classical metabolism pathways, other pathways may be important to type 2 diabetes that show a potential overlap with type 1 diabetes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08587-5.

Chemotherapy agents reduce protein synthesis and ribosomal capacity in myotubes independent of oxidative stress

Chemotherapeutic agents (CAs) are first-line antineoplastic treatments against a wide variety of cancers. Despite their effectiveness in halting tumor progression, side effects associated with CAs promote muscle loss by incompletely understood mechanisms. To address this problem, we first identified how oxidative stress impairs protein synthesis in C2C12 myotubes. Transient elevations in reactive oxygen species (ROS) resulted in protein synthesis deficits and reduced ribosomal (r)RNA levels. Oxidative stress did not reduce rRNA gene (rDNA) transcription, but it caused an increase in rRNA and protein oxidation. To determine whether CAs affect protein synthesis independent of oxidative stress, we exposed myotubes to Paclitaxel (PTX), Doxorubicin (DXR), or Marizomib (Mzb) at doses that did result in elevated ROS levels (sub-ROS). Exposure to CAs reduced protein synthesis and rRNA levels, but unlike oxidative stress, sub-ROS exposures impaired rDNA transcription. These results indicate that although oxidative stress disrupts protein synthesis by compromising ribosomal quantity and quality, CAs at sub-ROS doses compromise protein synthesis and ribosomal capacity, at least in part, by reducing rDNA transcription. Therefore, CAs negatively impact protein synthesis by causing oxidative stress in addition to directly reducing the ribosomal capacity of myotubes in a ROS-independent manner.

Reduced rDNA transcription diminishes skeletal muscle ribosomal capacity and protein synthesis in cancer cachexia

Muscle wasting in cancer is associated with deficits in protein synthesis, yet, the mechanisms underlying this anabolic impairment remain poorly understood. The capacity for protein synthesis is mainly determined by the abundance of muscle ribosomes, which is in turn regulated by transcription of the ribosomal (r)RNA genes (rDNA). In this study, we investigated whether muscle loss in a preclinical model of ovarian cancer is associated with a reduction in ribosomal capacity and was a consequence of impaired rDNA transcription. Tumor bearing resulted in a significant loss in gastrocnemius muscle weight and protein synthesis capacity, and was consistent with a significant reduction in rDNA transcription and ribosomal capacity. Despite the induction of the ribophagy receptor NUFIP1 mRNA and the loss of NUFIP1 protein, in vitro studies revealed that while inhibition of autophagy rescued NUFIP1, it did not prevent the loss of rRNA. Electrophoretic analysis of rRNA fragmentation from both in vivo and in vitro models showed no evidence of endonucleolytic cleavage, suggesting that rRNA degradation may not play a major role in modulating muscle ribosome abundance. Our results indicate that in this model of ovarian cancer-induced cachexia, the ability of skeletal muscle to synthesize protein is compromised by a reduction in rDNA transcription and consequently a lower ribosomal capacity. Thus, impaired ribosomal production appears to play a key role in the anabolic deficits associated with muscle wasting in cancer cachexia.

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

Energetic metabolism reprogramming is critical for cancer and immune responses. Current methods to functionally profile the global metabolic capacities and dependencies of cells are performed in bulk. We designed a simple method for complex metabolic profiling called SCENITH, for single-cell energetic metabolism by profiling translation inhibition. SCENITH allows for the study of metabolic responses in multiple cell types in parallel by flow cytometry. SCENITH is designed to perform metabolic studies ex vivo, particularly for rare cells in whole blood samples, avoiding metabolic biases introduced by culture media. We analyzed myeloid cells in solid tumors from patients and identified variable metabolic profiles, in ways that are not linked to their lineage or their activation phenotype. SCENITH's ability to reveal global metabolic functions and determine complex and linked immune-phenotypes in rare cell subpopulations will contribute to the information needed for evaluating therapeutic responses or patient stratification.

The science of puromycin: From studies of ribosome function to applications in biotechnology

Puromycin is a naturally occurring aminonucleoside antibiotic that inhibits protein synthesis by ribosome-catalyzed incorporation into the C-terminus of elongating nascent chains, blocking further extension and resulting in premature termination of translation. It is most commonly known as a selection marker for cell lines genetically engineered to express a resistance transgene, but its additional uses as a probe for protein synthesis have proven invaluable across a wide variety of model systems, ranging from purified ribosomes and cell-free translation to intact cultured cells and whole animals. Puromycin is comprised of a nucleoside covalently bound to an amino acid, mimicking the 3′ end of aminoacylated tRNAs that participate in delivery of amino acids to elongating ribosomes. Both moieties can tolerate some chemical substitutions and modifications without significant loss of activity, generating a diverse toolbox of puromycin-based reagents with added functionality, such as biotin for affinity purification or fluorophores for fluorescent microscopy detection. These reagents, as well as anti-puromycin antibodies, have played a pivotal role in advancing our understanding of the regulation and dysregulation of protein synthesis in normal and pathological processes, including immune response and neurological function. This manuscript reviews the current state of puromycin-based research, including structure and mechanism of action, relevant derivatives, use in advanced methodologies and some of the major insights generated using such techniques both in the lab and the clinic.

A Plant Biologist's Toolbox to Study Translation

Across a broad range of species and biological questions, more and more studies are incorporating translation data to better assess how gene regulation occurs at the level of protein synthesis. The inclusion of translation data improves upon, and has been shown to be more accurate than, transcriptional studies alone. However, there are many different techniques available to measure translation and it can be difficult, especially for young or aspiring scientists, to determine which methods are best applied in specific situations. We have assembled this review in order to enhance the understanding and promote the utilization of translational methods in plant biology. We cover a broad range of methods to measure changes in global translation (e.g., radiolabeling, polysome profiling, or puromycylation), translation of single genes (e.g., fluorescent reporter constructs, toeprinting, or ribosome density mapping), sequencing-based methods to uncover the entire translatome (e.g., Ribo-seq or translating ribosome affinity purification), and mass spectrometry-based methods to identify changes in the proteome (e.g., stable isotope labeling by amino acids in cell culture or bioorthogonal noncanonical amino acid tagging). The benefits and limitations of each method are discussed with a particular note of how applications from other model systems might be extended for use in plants. In order to make this burgeoning field more accessible to students and newer scientists, our review includes an extensive glossary to define key terms.

Measuring protein synthesis with SUnSET: a valid alternative to traditional techniques?

Protein synthesis rates commonly are measured using isotopic tracers to quantify the incorporation of a labeled amino acid into muscle proteins. Here we provide evidence supporting our hypothesis that the nonisotopic SUnSET technique is a valid and accurate method for the measurement of in vivo changes in protein synthesis at the whole-muscle and single-muscle fiber levels.

Hepatic protein synthetic activity in vivo after ethanol administration

Hepatic protein synthetic activity in vivo was measured by the incorporation of [3H]puromycin into elongating nascent polypeptides of rat liver to form peptidyl-[3H]puromycin. Our initial experiments showed that saturating doses of [3H]puromycin were achieved at 3-6 mumol/100 g body weight, and that maximum labeling of nascent polypeptides was obtained 30 min after injection of the labeled precursor. Labeled puromycin was found to be suitable for measuring changes in the status of protein synthesis, since the formation of the peptidyl-[3H]puromycin was decreased in fasted animals and was increased in rats pretreated with L-tryptophan. [3H]Puromycin incorporation into polypeptides was then measured after acute ethanol administration as well as after prolonged consumption of ethanol which was administered as part of a liquid diet for 31 days. Acute alcohol treatment caused no significant change in [3H]puromycin incorporation into liver polypeptides. In rats exposed to chronic ethanol feeding, peptidyl-[3H]puromycin formation, when expressed per mg of protein, was slightly lower compared to pair-fed controls, but was unchanged compared to chow-fed animals. When the data were expressed per mg of DNA or per 100 g body wt, no differences in protein synthetic activity were observed among the three groups. These findings indicate that neither acute nor chronic alcohol administration significantly affects protein synthetic activity in rat liver. They further suggest that accumulation of protein in the liver, usually seen after prolonged ethanol consumption, is apparently not reflected by an alteration of hepatic protein synthesis.

Measurement of protein synthetic activity by determination of peptidyl[3H]puromycin formation in liver slices after ethanol administration

We investigated the utility of [3H]puromycin as an alternate and adjunct precursor to amino acids for measuring protein synthetic activity in rat liver slices. Slices were incubated in the presence of either [3H]puromycin or radiolabeled valine to compare the incorporation of these isotopic precursors into nascent hepatocellular proteins. Compared to liver slices from controls, comparable decreases in the incorporation of both [3H]puromycin and labeled valine were observed in experiments using slices from fasted rats and in slices preincubated with 25 mM ethanol. Radiolabeling of nascent polypeptides with either [3H]puromycin or labeled valine in liver slices from rats fed a liquid diet containing ethanol was also decreased compared to slices from pair-fed control and chow-fed animals. Our results demonstrated the validity of using [3H]puromycin to detect changes in protein synthetic activity under these conditions. The potential advantage of using [3H]puromycin for in vivo studies is discussed.

Measurement of the protein-synthetic activity in vivo of various tissues in rats by using [3H]Puromycin

The validity of a new technique was examined for estimating the protein-synthetic activity of various tissues in vivo. The basic assumption underlying the method is that the number of peptide chains growing on each active ribosome would increase as the protein-synthetic activity of each tissue increases. The principle of the procedure, which was devised originally by Wool & Kurihara [(1967) Proc. Natl. Acad. Sci. U.S.A. 58, 2401-2407] to determine in vitro the number of functional ribosomes in skeletal muscle, is as follows. Puromycin is known to bind easily to the C-terminal end of the growing peptide on ribosomes and thus stop further chain elongation. Hence, if the number of puromycin molecules attached to the nascent peptide is determined by using radioactive puromycin as a tracer, one can estimate the number of growing peptides, i.e. the activity of tissue protein synthesis. By using this technique, it is shown that both starvation and the feeding of a protein-free diet caused marked decreases in the relative rate of formation of peptidyl-puromycin, i.e. activity of protein synthesis in liver, skeletal muscle, heart, spleen, testis, lung, kidney and intestine.

Number and activity of active ribosomes in bacterial polyribosomes

Polyribosomes were isolated from Baccillus licheniformis, grown at 37 and 46 degrees C, and from Bacillus stearothermophilus, grown at 46 and 55 degrees C. The polyribosomes were incubated with either [3H]puromycin or [14C]phenylalanine. The number of active ribosomes (i.e. those to which growing polypeptide chains are attached) was calculated from the amount of [3H]peptidyl-puromycin formed. The activity of an active ribosome (i.e. the total number of amino acid molecules incorporated/unit time per active ribosome) was calculated from the uptake of [14C]phenylalanine. The number of active ribosomes per migrogram of RNA was as follows: for B. licheniformis, 1.66 X 10(12) and 1.72 X 10(12) at 37 and 46 degrees C respectively; for B. stearothermophilus, 2.59 X 10(12) at 46 and 55 degreesC respectively. The activity per active ribosome was as follows: for B. licheniformis, 0.61 and 0.05 at 37 and 46 degrees C respectively; for B. stearothermophilus, 0.58 and 0.42 at 46 and 55 degrees C respectively.

The regulation of protein synthesis in animal cells by serum factors

We have investigated the regulation of protein synthesis in animal cells by serum factors. Withdrawal of serum from the medium of actively dividing Vero cells resulted in an immediate decline in the rate of peptide chain elongation (Hassell and Engelhardt, 1973). Assay of elongation factor I (EFI) activity in the post-ribosomal supernatant as well as that associated with the ribosomes revealed that serum deprivation resulted also in reduction in the activity of this factor. The decline in the activity of EFI after serum deprivation occurred to the same extent and at the same time as the decline in the in vivo rate of protein synthesis and the in vitro peptide synthetic capacity of cell-free extracts. A temporal correlation therefore exists among the in vivo rate of protein synthesis, the peptide synthetic activity of cell-free extracts, and the activity of EFI. The activity of peptidyl transferase was not altered by serum deprivation. The loss of extract peptide synthetic activity resulting from serum deprivation was reversible since serum addition to previously serum-starved cultures resulted in full restoration of activity for polyphenylalanine (polyPhe) synthesis within 3 h. Moreover, RNA synthesis was not required for this turn-on of polyPhe synthesis. Vased on these data we conclude that a translational control mechanism is operative in Vero cells deprived of serum.

Plant desiccation: polysome loss not due to ribonuclease

During desiccation of the drought-tolerant moss Tortula ruralis polysome levels decline substantially before any increase in ribonuclease activity is observed. Furthermore, ribosomes in the desiccated moss are not complexed with messenger RNA fragments. It is concluded that ribosome runoff and failure to re-form an initiation complex mediate polysome loss during desiccation.

Osmotic regulation of alpha-amylase synthesis and polyribosome formation in aleurone cells of barley

Water stress inhibits the gibberellic acid (GA(3))-induced synthesis of alpha-amylase in aleurone layers of barley (Hordeum vulgare L.). Electron microscope evidence indicates that the effect of water stress induced by 0.6 M solutions of polyethylene glycol (PEG) is to reduce the binding of ribosomes to the endoplasmic reticulum. This was confirmed by sucrose density gradient centrifugation of polyribosome preparations from stressed cells. The reduction in polyribosome formation does not result from reduced ribosome activity as measured by [(3)H]peptidylpuromycin formation. Thus, calculation of percent active ribosomes shows that osmoticum has little effect on the ability of ribosomes to incorporate puromycin into nascent protein. Water stress does not cause a marked decrease in the total RNA level of aleurone cells. Estimates of total RNA in postmitochondrial supernatant fractions from stressed cells show only a reduction of 8-9% relative to the control. Membrane synthesis measured by [(14)C]choline incorporation is depressed by 15% in cells stressed with 0.6 M PEG for 2.5 hours.

Mechanism of action of a microsomal inhibitor of protein synthesis potentiated by oxidized glutathione

Extracts of microsomal fractions cause an inhibition of protein synthesis that is most pronounced in the presence of 0.1mm-GSSG and 0.01mm-GTP, and is abolished by thiol or 0.4mm-GTP (Scornik et al., 1967). Fractionation of microsomal extracts showed that this inhibition of protein synthesis was caused by an enzyme, nucleoside diphosphate phosphohydrolase. Direct inhibition of protein synthesis on detergent-treated polyribosomes by 0.1mm-GSSG was observed under conditions of GTP limitation induced by omission of a GTP-regenerating system, or addition of a nucleoside triphosphate diphosphohydrolase. Thus GSSG potentiated the inhibition of protein synthesis caused by an enzyme that promoted removal of GTP. The inhibition was abolished by adding 4mm-2-mercaptoethanol or 0.4mm-GTP. Nucleoside diphosphate phosphohydrolase was thought also to act by promoting removal of GTP, thus causing an inhibition of protein synthesis that was potentiated by GSSG.

Effects of infection with Diplococcus pneumoniae on synthesis of ribonucleic acids in rat liver

Rats infected with virulent Diplococcus pneumoniae developed a significant increase in the rate of incorporation of labelled orotate into hepatic RNA when compared with pair-fed controls inoculated with heat-killed organisms. The finding was readily detected in rats raised on either a low-protein diet (6% casein) or a diet containing adequate amounts of protein (18% casein). The increase in hepatic RNA synthesis was observed by 12h and was maximal by 16-20h after inoculation with the D. pneumoniae. Most of the infection-related increase in RNA synthesis was associated with the bound ribosomal RNA fraction of the liver. A small but less significant increase was observed in the synthesis of free ribosomal RNA. The increased synthesis of RNA in the liver of infected rats resulted in a marked elevation of the liver RNA/DNA ratio, the major increase being observed in concentration of bound ribosomal RNA fraction. When followed sequentially, the infection-related increase in synthesis of hepatic RNA was preceded by a flux of amino acids into liver and was followed by elevated synthesis rates of serum globulin proteins. These findings suggest that the infectious process was able to regulate hepatic RNA synthesis by altering the rate of transcription of new RNA. This mechanism was stimulated even in rats that had been severely depleted of body protein and amino acids by feeding them on a low-protein diet. The infection-related stimulation of liver RNA and protein synthesis thus appeared to take place at the expense of other body proteins.

Amino acid regulation of synthesis of ribonucleic acid and protein in the liver of rats

Weanling (23-day-old) rats were fed on either a low-protein diet (6% casein) or a diet containing an adequate amount of protein (18% casein) for 28 days. Hepatic cells from animals fed on the deficient diet were characterized by markedly lower concentrations of protein and RNA in all cellular fractions as compared with cells from control rats. The bound rRNA fraction was decreased to the greatest degree, whereas the free ribosomal concentrations were only slightly less than in control animals. A good correlation was observed between the rate of hepatic protein synthesis in vivo and the cellular protein content of the liver. Rates of protein synthesis both in vivo and in vitro were directly correlated with the hepatic concentration of individual free amino acids that are essential for protein synthesis. The decreased protein-synthetic ability of the ribosomes from the liver of protein-deprived rats was related to a decrease in the number of active ribosomes and heavy polyribosomes. The lower ribosomal content of the hepatocytes was correlated with the decreased concentration of essential free amino acids. In the protein-deprived rats, the rate of accumulation of newly synthesized cytoplasmic rRNA was markedly decreased compared with control animals. From these results it was concluded that amino acids regulate protein synthesis (1) by affecting the number of ribosomes that actively synthesize protein and (2) by inhibiting the rate of synthesis of new ribosomes. Both of these processes may involve the synthesis of proteins with a rapid rate of turnover.

Binding and translation of turnip-yellow-mosaic-virus ribonucleic acid by skeletal-muscle ribosomes from normal and diabetic rats

Ribosomes from skeletal muscle of diabetic rats were less active than normal ribosomes in protein synthesis directed by turnip-yellow-mosaic-virus RNA. The proportion of ribosomes from muscle of diabetic rats capable of binding turnip-yellow-mosaic-virus RNA was greater than normal, but there was no difference in the equilibrium constants for the binding reaction. The turnip-yellow-mosaic-virus RNA was bound preferentially to the small (40S) ribosomal subunit, whereas the decrease due to diabetes in its translation was associated with the large (60S) subunit. Thus the diminished capacity of ribosomes from muscle of diabetic rats to translate turnip-yellow-mosaic-virus RNA was not the result of decreased binding of the template.

Influence of amino acid supply on ribosomes and protein synthesis of perfused rat liver

1. The livers of rats were perfused in situ with medium containing mixtures of amino acids in multiples of their concentration in normal rat plasma. The incorporation of labelled amino acid into protein of the liver and of the perfusing medium increased with increasing amino acid concentration. During 60min. perfusions, labelling of liver protein reached a plateau, and labelling of medium protein was inhibited when the initial concentration of the amino acid mixture was more than ten times the normal plasma value. 2. Examination of polysome profiles derived from livers perfused without amino acids in the medium showed that the number of large aggregates was decreased and the number of small aggregates, particularly monomers and dimers, was increased with time of perfusion. The addition of amino acids to the perfusion medium reversed this polysome shift to an extent that was dependent on the initial concentration of amino acids. Polysome profiles derived from livers perfused for 60min. with ten times the normal plasma concentration of amino acids were essentially the same as the polysome profiles of normal non-perfused livers. 3. The ability of ribosome preparations from perfused livers to incorporate amino acids into protein in vitro decreased with increasing time of perfusion when no amino acids were added to the medium, but increased as the concentration of amino acids in the perfusion medium was increased. 4. The ability of cell sap from perfused livers to support protein synthesis in vitro was not influenced by the amino acid concentration of the perfusion medium. 5. Livers were perfused for 60min. with medium containing amino acid mixtures at ten times the normal plasma concentration but deficient in one amino acid. Maximal incorporation of labelled amino acid into liver protein, the stability of the polysome profile and the ability of ribosome preparations to incorporate amino acids into protein were found to depend on the presence of 11 amino acids: arginine, asparagine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, threonine, tryptophan and valine. A mixture of these 11 amino acids, at ten times their normal plasma concentration, stimulated the incorporation of labelled amino acid into liver protein, stabilized the polysome profile and increased the ability of ribosome preparations to incorporate amino acids into protein to the same extent as the complete mixture. 6. It is concluded that the availability of certain amino acids plays an important role in the control of protein synthesis, possibly by stimulating the ability of ribosomes to become, and to remain, attached to messenger RNA.