An analysis of rates of polypeptide chain elongation in avian liver explants following in vivo estrogen treatment. I. Determination of average rates of polypeptide chain elongation

The role of RNA modifications in the regulation of tRNA cleavage

Transfer RNA (tRNA) have been harbingers of many paradigms in RNA biology. They are among the first recognized noncoding RNA (ncRNA) playing fundamental roles in RNA metabolism. Although mainly recognized for their role in decoding mRNA and delivering amino acids to the growing polypeptide chain, tRNA also serve as an abundant source of small ncRNA named tRNA fragments. The functional significance of these fragments is only beginning to be uncovered. Early on, tRNA were recognized as heavily post-transcriptionally modified, which aids in proper folding and modulates the tRNA:mRNA anticodon-codon interactions. Emerging data suggest that these modifications play critical roles in the generation and activity of tRNA fragments. Modifications can both protect tRNA from cleavage or promote their cleavage. Modifications to individual fragments may be required for their activity. Recent work has shown that some modifications are critical for stem cell development and that failure to deposit certain modifications has profound effects on disease. This review will discuss how tRNA modifications regulate the generation and activity of tRNA fragments.

Transimulation - protein biosynthesis web service

Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation – a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes’ movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.

A comprehensive, quantitative, and genome-wide model of translation

Translation is still poorly characterised at the level of individual proteins and its role in regulation of gene expression has been constantly underestimated. To better understand the process of protein synthesis we developed a comprehensive and quantitative model of translation, characterising protein synthesis separately for individual genes. The main advantage of the model is that basing it on only a few datasets and general assumptions allows the calculation of many important translational parameters, which are extremely difficult to measure experimentally. In the model, each gene is attributed with a set of translational parameters, namely the absolute number of transcripts, ribosome density, mean codon translation time, total transcript translation time, total time required for translation initiation and elongation, translation initiation rate, mean mRNA lifetime, and absolute number of proteins produced by gene transcripts. Most parameters were calculated based on only one experimental dataset of genome-wide ribosome profiling. The model was implemented in Saccharomyces cerevisiae, and its results were compared with available data, yielding reasonably good correlations. The calculated coefficients were used to perform a global analysis of translation in yeast, revealing some interesting aspects of the process. We have shown that two commonly used measures of translation efficiency – ribosome density and number of protein molecules produced – are affected by two distinct factors. High values of both measures are caused, i.a., by very short times of translation initiation, however, the origins of initiation time reduction are completely different in both cases. The model is universal and can be applied to any organism, if the necessary input data are available. The model allows us to better integrate transcriptomic and proteomic data. A few other possibilities of the model utilisation are discussed concerning the example of the yeast system.

Translation is the production of proteins by decoding mRNA produced in transcription, and is a part of the overall process of gene expression. Although the general theoretical background of translation is known, the process is still poorly characterised at the level of individual proteins. In particular, the quantitative parameters of translation, such as time required to complete it or the number of protein molecules produced from a transcript during its lifetime, are extremely difficult to measure experimentally. To overcome this problem, we developed a computational model that, on the basis of only few datasets and general assumptions, measures quantitatively the translational activity at the level of individual genes. We discussed it concerning the example of the yeast system; however, it can be applied to any organism of known genome. We used the obtained results to study the general characteristics of the yeast translational system, revealing the diversity of strategies of gene expression regulation. We exemplified and discussed other possible ways of model utilisation, as it may help in examining protein-protein interactions, metabolic pathways, gene annotation, ribosome queueing, protein folding, and translation initiation. It also may be crucial for better integration of cell-wide, high-throughput experiments.

Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray

Exposure to a variety of compounds with estrogenic activity has been shown to interfere with normal developmental and reproductive processes in various vertebrate species. The aim of this study was to determine the transcriptional profile of the natural estrogen, 17 beta-estradiol, and three synthetic estrogenic compounds (4-nonylphenol, bisphenol A, ethinylestradiol) in the liver of common carp, using a custom cDNA microarray. For that purpose, fish were aqueously exposed to three concentrations of each chemical for 24 or 96 h. Microarray analysis revealed that a total of 185 different gene transcripts were differentially expressed following exposure to at least one of the estrogen(-like) concentrations. We were able to identify a common set of 28 gene fragments, whose expression was significantly modified in the same way by the three xenoestrogens and 17 beta-estradiol. Although several of these gene expression effects corroborated past literature data, we also discovered some novel target genes of (xeno)estrogen exposure, providing interesting insights into the molecular basis of estrogenic effects. In addition, each of the four compounds induced gene expression changes that were not, or only partially, shared by the other chemicals, suggesting that not all chemicals with estrogenic activity act alike. These results demonstrate the potential of our custom Cyprinus carpio microarray to detect common estrogen-like activity as well as to identify unique compound-associated effects of (estrogenic) endocrine disruptors in fish.

Estrogen induces the assembly of a multiprotein messenger ribonucleoprotein complex on the 3'-untranslated region of chicken apolipoprotein II mRNA

UV cross-linking was used to identify estrogen-induced hepatocyte proteins that bind to apoII mRNA. Probes spanning the entire message revealed the presence of eight estrogen-induced proteins cross-linked to the 3'-untranslated region (UTR), but not to the coding region or the 5'-UTR. Two estrogen-induced proteins of 132 and 50 kDa were either absent or barely detectable in control animals, whereas six additional proteins of 93, 83, 74, 65, 58, and 45 kDa were clearly present in control animals and increased 2-5-fold by estrogen. A similar profile of estrogen-induced proteins was seen with the 3'-UTRs of the estrogen-regulated mRNAs for apoB and vitellogenin II, but not with the 3'-UTRs of the non-estrogen-regulated mRNAs for apoA-I and glyceraldehyde-phosphate dehydrogenase. These findings indicate that the estrogen-induced proteins discriminate among mRNAs and suggest that they interact selectively with the family of estrogen-regulated mRNAs. The estrogen-induced proteins are found in the cytoplasmic fraction of liver extracts, and a subset of them are also found in adrenal glands, testes, heart, brain, and kidneys, but they are estrogen-induced only in the liver. Deletion analysis defined a 150-nucleotide region of the apoII 3'-UTR that is necessary for maximal binding of the estrogen-induced proteins. An internal deletion of endonucleolytic cleavage sites previously identified within the apoII 3'-UTR selectively reduced the binding of the 58-kDa protein. These findings reveal remarkable complexity in estrogen-stimulated protein-RNA interactions within the 3'-UTRs of estrogen-regulated mRNAs. These proteins may participate in the mRNA degradation process or in other aspects of cytoplasmic mRNA metabolism that accompany estrogen-stimulated vitellogenesis.

Regulation of transcription by translational components in coupled translation-transcription cell-free system

A coupled translation-transcription cell-free system was established from eukaryotic cells. The biosynthetic activity of this coupled system closely resembles the synthetic behavior of cells in vivo, and exhibits regulatory phenomena similar to that of intact cells. The translational system consists of rabbit reticulocyte lysate, or its components fractionated by centrifugation. The transcriptional portion consists of cockerel liver nuclei. Incorporation of amino acids into protein by the coupled system is linear for hours. Similarly, transcription in the coupled system is continuous for hours and is proportional with time. More than 90% of the transcriptional products are secreted into the incubation medium. The components of the translational system influence and regulate transcriptional activities. In the presence of ribosomes the nuclei transcribe mostly poly(A)+ RNA with alpha-amanitin sensitivity consistent with activation of RNA polymerase II. Hybrid selection experiments demonstrate authentic preproalbumin mRNA among the transcriptional products. The putative mRNA secreted into the medium in the coupled system is found on polysomes, indicating translation of de novo synthesized message. Addition of excess reticulocyte mRNP to the medium of the coupled system results in transcription of primarily ribosomal RNA, 5S RNA, and tRNA, the products of RNA polymerases I and III. These activities closely imitate the behavior of liver in vivo under conditions of nutritional shifts or hormonal influences. The coupled system transcribes, processes, and transports substantial quantities of RNA, about 1.6 micrograms/10(6) nuclei/h. Thus, a coupled system has been established that lends itself to the exploration of regulatory interactions of cell components as it appears to closely resemble the in vivo situation.

Regulation of protein synthesis at the elongation stage. New insights into the control of gene expression in eukaryotes

There are many reports which demonstrate that the rate of protein biosynthesis at the elongation stage is actively regulated in eukaryotic cells. Possible physiological roles for this type of regulation are: the coordination of translation of mRNA with different initiation rate constants; regulation of transition between different physiological states of a cell, such as transition between stages of the cell cycle; and in general, any situation where the maintenance of a particular physiological state is dependent on continuous protein synthesis. A number of covalent modifications of elongation factors offer potential mechanisms for such regulation. Among the various modifications of elongation factors, phosphorylation of eEF-2 by the specific Ca2+calmodulin-dependent eEF-2 kinase is the best studied and perhaps the most important mechanism of regulation of elongation rate. Since this phosphorylation is strictly Ca(2+)-dependent, and makes eEF-2 inactive in translation, this mechanism could explain how changes in the intracellular free Ca2+ concentration may regulate elongation rate. We also discuss some recent findings concerning elongation factors, such as the discovery of developmental stage-specific elongation factors and the regulated binding of eEF-1 alpha to cytoskeletal elements. Together, these observations underline the importance of the elongation stage of translation in the regulation of the cellular processes essential for normal cell life.

Vitellogenesis in the lizard Lacerta vivipara jacquin. I. Purification and partial characterization of plasma vitellogenin

The polypeptide moiety of lizard plasma vitellogenin was reproducibly dissociated and separated by SDS-PAGE into two subunits: Vg alpha 2-2.2 X 10(5) Da and Vg beta 1-1.1 X 10(5) Da. In estrogenized females, active incorporation of inorganic 32P into both vitellogenin chains present in the plasma, and in the culture medium of the liver, was identified following autoradiography of SDS-polyacrylamide gels. Lacerta vivipara vitellogenin was isolated from pooled plasma collected from heavily estrogenized males by the two-step precipitation procedure of H. S. Wiley, L. Opresko, and R. A. Wallace, (1980, Anal. Biochem. 97, 145-152), followed by chromatography on DEAE-cellulose. This preparation of L. vivipara vitellogenin was of sufficient purity to generate in rabbits an immune serum which cross-reacted very slightly with plasma free of vitellogenin (rocket immunoelectrophoresis). Using the double immunodiffusion procedure it was shown that the anti-vitellogenin serum recognized identical antigenic determinants in plasma from a vitellogenic female or from estrogenized lizards, and in crude vitellus. The immunodetection of L. vivipara native vitellogenin consistently allowed two circulating forms to be distinguished. After autoradiography of a rocket immunoelectrophoresis plate it was demonstrated that both native forms had incorporated inorganic 32P into the polypeptide moiety and/or the phospholipid moiety.

Influence of fasting and refeeding on the elongation step of protein synthesis in rat liver of young (3M) and aging (18M) animals

The in vitro binding capacity for AA-tRNA of ribosomes, catalysed by EF1 enzyme, was studied in livers of rats, which had been starved for 5 days and re-fed for 3, 9, and 24 hours. The experiments were carried out with 3 and 18-month-old rats. The results were compared to those obtained with normally fed rats of the same ages. For both age groups, there was a similar change in the binding capacity, including a return to normal values after 24 hours of refeeding. When ribosomes of old control animals were treated with different enzymes, we obtained lower binding activities for all the experimental groups than in homologous cell-free systems (ribosomes and EF1 isolated from the same group). The ribosomes of young animals, tested in the presence of different enzymes, display an increased binding capacity, when the enzymes used were those of old (control and re-fed) animals. The recovery of the catalytic activity of EF1 on the binding process was observed after 9 hours in old animals, whereas it was not seen for young re-fed animals at that time of refeeding. EF1 seems to play an important role in the adaptation of older animals to fasting and refeeding.

Differential inhibition of protein synthesis: a possible biochemical mechanism of thalidomide teratogenesis

A theory concerning the chemical and biochemical mechanisms of thalidomide teratogenesis is presented. A considerable body of evidence suggests that the glutarimide ring of thalidomide may exert its biological activity because of its resemblance to the imide pyrimidines thymine and uracil. In addition to the glutarimide ring, thalidomide contains a moderately reactive phthalimide moiety, which allows the spontaneous formation of various glutarimide derivatives in fetal tissues. A model is proposed in which the phthalimide group reacts with small nucleophiles, most likely the polyamines, to produce a derivative(s) having a similar biochemical potential to that of cycloheximide, a glutarimide which is a powerful inhibitor of the elongation phase of protein synthesis. Interference in the elongation phase results in the selective inhibition of the translation of messages which have a high translational efficiency. Evidence is reviewed concerning the differential inhibition or protein synthesis by cycloheximide and the effects of this inhibition on various biochemical and biological processes which are critical during development and differentiation. A similar biochemical activity by the putative thalidomide derivative(s) could explain its extreme teratogenic potential. A number of parallels between the biological effects of thalidomide and cycloheximide are discussed which support the idea that a similar biochemical activity is involved. The theory readily explains many of the observed biological effects of thalidomide including the large difference between fetal and adult toxicity. In addition, evidence is reviewed which suggests that the teratogenic properties of a number of drugs which are structurally related to thalidomide may have a common chemical basis due to the similarity of their imide core structures to thymine and uracil.

Dietary regulation of levels of active mRNA coding for amylase and serine protease zymogens in the rat pancreas

The mechanism by which changes in diet mediate levels of exportable enzymes and proenzymes in pancreatic tissue were studied in rats. The relative levels of mRNA coding for pancreatic amylase, lipase, procarboxypeptidases A and B, and the family of serine protease zymogens have been determined by the ability of isolated RNA to direct the synthesis of these products in a high-fidelity micrococcal nuclease-treated reticulocyte-lysate translation system. Translation products synthesized in vitro correlated directly with products synthesized in vivo in pancreatic lobules. Dietary adaptation was observed when dietary carbohydrate was increased from 0 to 58% at the expense of protein (81-23%). The increase in dietary carbohydrate over this range resulted in a 2-fold increase in amylase synthesis in pancreatic lobules and a 1.8-fold increase in mRNA-directed synthesis of amylase in the translation system in vitro. Concomitant with the decrease in dietary protein, synthesis of serine protease zymogens in pancreatic lobules and in the system in vitro decreased by approximately 50%. Over this range of dietary manipulation, ratios of amylase to serine proteases showed a 3.6-fold change. When dietary carbohydrate was further increased to 81% and protein reduced to 0, non-adaptive changes were observed since there was a decrease in amylase synthesis under conditions both in vivo and in vitro. mRNAs coding for pancreatic lipase and procarboxypeptidases A and B were unaffected by the dietary changes. These findings indicate that nutritional regulation in the tissue levels of pancreatic enzymes and proenzymes is mediated by changes in the content of active cytoplasmic mRNAs.

Characterization and comparative immunoreactivity of antibody to newt (T. cristatus) globins

Rabbit antisera to newt (T. cristatus) globin were produced by repeated injections of globin and antiglobin antibodies purified by chromatography on globin-Sepharose 4B. Ouchterlony and SDS PAGE analysis indicated that the material eluted from the affinity column was rabbit IgG. The antiglobin antibodies tested by immunodiffusion and ELISA cross-reacted with native hemoglobin and globin from T. cristatus and to varying extents with globins of N. viridescens, R. pipiens and X. laevis, but not with human globin. The degree of cross-reactivity appeared to parallel the evolutionary relatedness of these species, suggesting common antigenic determinants among globins of various vertebrate species.