Messenger RNA translation in the presence of homologous and heterologous tRNA

Protein folding and tRNA biology

Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

Prediction of growth with kinetics of cell-free translation systems

The kinetics of cell-free translation systems containing as main components washed rat liver polysomes and muscle cell sap from a muscle piece of the proband, can be used for predicting body growth rate or muscle tissue growth in cattle and swine. A muscle biopsy from the hindquarters of animals aged about 45 days is the source of the muscle fraction. It introduces into the translation systems the required aminoacylated tRNA and translational initiating and elongating factors containing the muscle cell sap fraction of the proband. Based on a polynomial regression of the type [Formula: see text] the coefficient of the multiple correlation between either the growth rate or the lifetime-related muscle mass (Y) of the carcass of boars aged 195±19 days or of bulls aged 450±20 days and the translational kinetics (T) is 0.60-0.8. A generalized expression of the relationship between growth criterions Y (muscle tissue growth rate or nutritional energy expenditure for the growth rate) is [Formula: see text] where S y (2) is the variance of the growth criterion; L is a constant, its value is approximately 2; and f(T) is the function mentioned above. If T is measured in sires and Y in male offsprings, the coefficient of the genetic correlation between a linear combination of Ti and Y is 0.6-0.9.

The importance of tRNA for the in vitro cell-free translation of messenger RNA isolated from the malaria parasite Plasmodium lophurae

Preliminary studies had indicated the inadequacy of the wheat germ and rabbit reticulocyte cell-free translation systems for the in vitro translation of mRNA isolated from Plasmodium lophurae. To identify the factors which are important for the efficient translation of parasite proteins, an homologous system was established using polysomes, the pH 5 fraction, and tRNA prepared from p. lophurae. For comparison, the same components were isolated from the host duck reticulocytes and tested. The effect of each of these factors was evaluated by analysis of the translation products and by comparison with products synthetized in vivo. The results indicated that P. lophurae tRNA had a marked stimulatory effect on the synthesis of parasite proteins while it inhibited the synthesis of host proteins. Duck reticulocyte tRNA could not be used as a substitute for the parasite tRNA. Based on these findings, a commercially available rabbit reticulocyte system was supplemented with P. lophurae tRNA, which markedly increased the efficiency of translation of P. lophurae proteins by this system.

Effect of tRNA pool balance on rate and uniformity of elongation during translation of fibroin mRNA in a reticulocyte cell-free system

Unsuccessful attempts to synthesize complete fibroin chains in vitro were previously made in heterologous cell-free system [3]. In the present work, we succeeded to obtain complete translation of purified fibroin mRNA in a rabbit reticulocyte lysate. Whilst this work was being completed [1], similar results were published by Lizardi et al. [4]. The synthesis of full-sized molecules of fibroin (M.W. 360,000) was achieved by adding tRNA from the posterior silk gland to the cell-free system. With tRNA from other sources, both the translation rate and the amount of complete fibroin chains dropped. This effect of tRNA is situated at the elongation levels. Analysis of cell-free synthesized products by polyacrylamide gel electrophoresis shows that smaller discrete polypeptides are accumulated after 120 minutes of incubation. These polypeptides correspond to growing fibroin chains. This pattern of translation products suggests that elongation might decelerate at specific sites of the fibroin mRNA. These results show that a tRNA pool adjusted to mRNA codon frequency is required to obtain the maximal average elongation rate. A stochastic model based on random acceptance of tRNA at the ribosomal A site for the codon-anticodon recognition process can explain this phenomenon. It can also explain the occurrence of the unfinished discrete fibroin polypeptides during in vitro translation.

Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model

Neither a dynamic nor an energetic approach of the translation process has taken into account that intracellular levels of iso-tRNA species are adapted or adjusted to the codon frequency of mRNA being decoded (Bombyx mori silk gland, rabbit reticulocyte). A critical study of available experimental data suggests that the average elongation rate of a protein is maximized in the presence of an adapted tRNA population, usually an homologous tRNA. In addition, the amount of synthesized protein parallels that of corresponding mRNA. Other evidences--including in vitro and in vivo elongation assays with fibroin mRNA--show that individual elongation rates are not uniform. Pauses occur at certain sites of the mRNA chain. The relative lifetime of these pauses depends on the tRNA pool used. Finally, it appears that translation accuracy also depends on the balanced tRNA population. We propose to explain these different effects by using a codon-anticodon recognition model, called "trial and error system" based on a stochastic processing of the ribosome. Accordingly, various acylated tRNA species which surround a ribosome randomly encounter the receptor A site. Every trapped tRNA species is tested for a proper pairing with the codon to be recognized at the level of a comparator or discriminator function. If the pairing is correct, transpeptidation becomes irreversible. If not, the aminoacyl-tRNA is rejected and another randomly trapped tRNA is processed in turn. Mathematical analysis of this model shows that the mean number of trials used for translating the whole sequence of a mRNA is minimized when the proportion of different iso-tRNA species is correlated with the square root of codon frequency. Quantitations of reticulocyte tRNA support such a parabolic relation. Our translation system model brings some light into the role of tRNA adaptation for optimizing translation efficiency, i.e. maximizing both speed and accuracy. Some consequences of the model are discussed.

Starvation phase of Physarum polycephalum: characterization of transfer ribonucleic acid

We have begun a series of studies designed to characterize gene expression during differentiation in the slime mold Physarum polycephalum. This work concerns the starvation phase of the sporulation sequence and describes some of the quantitative changes which occur in plasmodial constituents during the 3-day starvation period and also describes alterations in the transfer ribonucleic acid (tRNA) population. The results show that whereas the plasmodial tRNA content decreased by 75% during starvation, concurrent de novo synthesis of tRNA also occurred, and they also show that overall amino acid acceptor activity of the starvation-phase tRNA population did not differ significantly from that found in the growth phase. Of the 19 starvation-phase tRNA families assayed, however, 6 were found to have consistently lower acceptor activities than did their growth-phase counterparts. Reverse-phase (RPC-5) chromatographic analysis of five of those families failed to reveal any major differences between growth- and starvation-phase isoacceptors. The data suggest that the depletion and resynthesis of tRNA during the starvation phase results in a quantitative alteration in the composition of the tRNA population and that the alteration is tRNA family and not tRNA isoacceptor specific.

Starvation phase of Physarum polycephalum: characterization of transfer ribonucleic acid

We have begun a series of studies designed to characterize gene expression during differentiation in the slime mold Physarum polycephalum. This work concerns the starvation phase of the sporulation sequence and describes some of the quantitative changes which occur in plasmodial constituents during the 3-day starvation period and also describes alterations in the transfer ribonucleic acid (tRNA) population. The results show that whereas the plasmodial tRNA content decreased by 75% during starvation, concurrent de novo synthesis of tRNA also occurred, and they also show that overall amino acid acceptor activity of the starvation-phase tRNA population did not differ significantly from that found in the growth phase. Of the 19 starvation-phase tRNA families assayed, however, 6 were found to have consistently lower acceptor activities than did their growth-phase counterparts. Reverse-phase (RPC-5) chromatographic analysis of five of those families failed to reveal any major differences between growth- and starvation-phase isoacceptors. The data suggest that the depletion and resynthesis of tRNA during the starvation phase results in a quantitative alteration in the composition of the tRNA population and that the alteration is tRNA family and not tRNA isoacceptor specific.

Analysis of messenger RNA coding for S100 protein in the mammalian brain

S100 protein is a brain-specific protein which is absent at birth and first appears in rabbit brain 2-3 days after birth. To determine how the synthesis of this brain-specific protein is regulated, mRNA was isolated from brain polysomes and assayed for S100 protein mRNA activity by in vitro translation in a heterologous cell-free system and immunoprecipitation of released polypeptides with rabbit anti-S100 protein antiserum. S100 protein mRNA was detected primarily in small polysomes containing five to eight ribosomes, and virtually no S100 protein mRNA was present in polysomes containing more than eight ribosomes. S100 protein mRNA was not detected in brain polysomes at stages prior to the induction of synthesis of S100 protein, i.e., in fetal brain or in 1-day neonates. The amount of S100 protein mRNA in polysomes of the cerebral cortex and cerebellum was measured to see if it correlated with the level of S100 protein in the two regions of adult brain. The cerebellum, which contained three to four times the level of S100 protein in the cerebral cortex, contained four times more S100 protein mRNA.

Adaptation of the tRNA population of maize endosperm for zein synthesis

Maize endosperm, 30 days after pollination is actively synthesizing zein, a storage protein containing high amounts of glutamine. leucine and alanine. Endosperm tRNAs have a higher accepting activity than embryo tRNAs for these three amino acids, but not for some other (control) amino acids. This increase in accepting activity is accompanied by a change in the distribution of the isoaccepting tRNA species corresponding to these three amino acids, but not of the isoacceptors corresponding to some other (control) amino acids. These results are in favor of the theory of functional adaptation of tRNA population.

Regulation of synthesis of a brain-specific protein in monolayer cultures of clonal rat glial cells

C6 cells were grown in monolayer culture under conditions permitting continued exponential cell division after attainment of a density at which extensive intercellular contacts were formed. An increase in the relative synthesis of S100 protein coincided with the time of formation of extensive intercellular contacts and preceded the onset of the stationary phase of growth by three generations. These observations suggested that the induction of S100 protein synthesis was mediated by cell contact and not by an arrest of cellular growth. The mechanism of this induction was first studied in a homologous non-initiating cell-free protein-synthesizing system from C6 cells, using fixed amounts of free amino acids or fully charged rat liver aminoacyl-tRNA as a source of precursors for protein synthesis. Real synthesis of total soluble proteins decreased as the cells progressed from logarithmic to stationary growth while synthesis of S100 protein increased during this period. The capacity of poly(A)+ RNA from logarithmic and stationary cultures to direct the synthesis of S100 protein was estimated in a cell-free protein-synthesizing system derived from wheat embryos. Increased synthesis of S100 protein in stationary cultures was directly correlated with an increase in translatable S100 protein mRNA.