Effects of growth rate on cell extract performance in cell-free protein synthesis

Cell-free protein synthesis is a useful research tool and now stands poised to compete with in vivo expression for commercial production of proteins. However, both the extract preparation and protein synthesis procedures must be scaled up. A key challenge is producing the required amount of biomass that also results in highly active cell-free extracts. In this work, we show that the growth rate of the culture dramatically affects extract performance. Extracts prepared from cultures with a specific growth rate of 0.7/h or higher produced approximately 0.9 mg/mL of chloramphenicol acetyl transferase (CAT) in a batch reaction. In contrast, when the source culture growth rate was 0.3/h, the resulting extract produced only 0.5 mg/mL CAT. Examination of the ribosome content in the extracts revealed that the growth rate of the source cells strongly influenced the final ribosome concentration. Polysome analysis of cell-free protein synthesis reactions indicated that about 22% of the total 70S ribosomes are in polysomes for all extracts regardless of growth rate. Furthermore, the overall specific production from the 70S ribosomes is about 22 CAT proteins per ribosome over the course of the reaction in all cases. It appears that rapid culture growth rates are essential for producing a productive extract. However, growth rate does not seem to influence specific ribosome activity. Rather, the increase in extract productivity is a result of a higher ribosome concentration. These results are important for cell-free technology and also suggest an assay for intrinsic in vivo protein synthesis activity.     

Ribosome subunit to polysome ratios affect the synthesis of rRNA in Drosophila cells

Many investigations have revealed that ribosome numbers increase in parallel with the growth rate of cells. Here we show that the absolute level of protein synthesis may not be the only factor influencing rRNA synthesis in a nondividing eukaryotic cell. Under conditions of complete (greater than 99%) inhibition of protein synthesis by four different antibiotics, there is a corresponding inhibition of rRNA synthesis. At lower levels of inhibition of protein synthesis (70%), a different effect of individual antibiotics on rRNA synthesis is observed. Cycloheximide and anisomycin, which cause a decrease in the free subunit pool due to a buildup of polysomes, stimulate rRNA synthesis, whereas puromycin and pactamycin, which cause an increase in the free subunit pool, cause a decrease in rRNA synthesis. These effects on rRNA synthesis are not solely due to a low level of completed proteins. Pactamycin treatment allows completed proteins to be made yet lowers rRNA labeling, while anisomycin treatment does not show synthesis of complete proteins yet increases rRNA labeling. The result suggest that eukaryotic cells may regulate ribosome synthesis in response to the number of free versus translating (polysomal) ribosomes as do Escherichia coli cells.     

Evidence for a high proportion of inactive ribosomes in slow-growing yeast cells.

From the protein and RNA content of Saccharomyces cerevisiae growing in different media we calculate that ribosome efficiency is changed: incorporation of amino acids into protein decreases from 8.8 amino acids/s per ribosome in fast-growing cells (0.54 doubling/h) to 5.2 amino acids/s per ribosome in slow-growing cells (0.30 doubling/h). We could not detect significant protein turnover in either fast-or slow-growing cultures, so the lower ribosome efficiency does not seem to be an artifact caused by changes in unstable protein production at different growth rates. Nor is the lower ribosome efficiency due to slower migration of ribosomes along mRNA: the times required to complete polypeptides of known molecular weights are the same in slow-growing cells as those previously determined for fast-growing cells [Waldron, Jund & Lacroute (1974) FEBS Lett. 46, 11-16]. We therefore deduce that ribosome efficiency changes in yeast because the fraction of ribosomes engaged in protein synthesis falls (from 84% in fast-growing cells to 50% in slow-growing cells.     

The kinetics of the incorporation of newly synthesized ribonucleic acid and protein into the ribosomes of the uterus of the oestrogen-stimulated immature rat.

The kinetics of the synthesis of the components of polyribosomes was investigated in the uterus of the immature rat responding to the administration of oestradiol-17 beta. The hormone brings about a rapid stimulation of the association of newly synthesized mRNA with uterine ribosomes, which is maximal 2-4 h after oestradiol administration and causes the aggregation of pre-existing ribosomes into polyribosomes. Despite the striking stimulation of rRNA synthesis 2-4 h after hormone treatment [Knowler & Smellie (1971) Biochem. J. 125, 605-614], the accumulation of new rRNA into ribosomes does not reach a peak until 12 h after administration. At this time, the incorporation of new ribosomal protein is also maximal. A second peak of incorporation of newly synthesized mRNA into polyribosomes follows the peak of ribosome synthesis and coincides with the oestrogen-activated synthesis of DNA.     

Rapid cytoplasmic turnover of yeast ribosomes in response to rapamycin inhibition of TOR

The target of rapamycin (TOR) pathway is the central regulator of cell growth in eukaryotes. Inhibition of TOR by rapamycin elicits changes in translation attributed mainly to altered translation initiation and repression of the synthesis of new ribosomes. Using quantitative analysis of rRNA, we found that the number of existing ribosomes present in a Saccharomyces cerevisiae culture during growth in rich medium rapidly decreases by 40 to 60% when the cells are treated with rapamycin. This process is not appreciably affected by a suppression of autophagy, previously implicated in degradation of ribosomes in eukaryotes upon starvation. Yeast cells deficient in the exosome function or lacking its cytoplasmic Ski cofactors show an abnormal pattern of rRNA degradation, particularly in the large ribosomal subunit, and accumulate rRNA fragments after rapamycin treatment and during diauxic shift. The exosome and Ski proteins are thus important for processing of rRNA decay intermediates, although they are probably not responsible for initiating rRNA decay. The role of cytoplasmic nucleases in rapamycin-induced rRNA degradation suggests mechanistic parallels of this process to nutrient-controlled ribosome turnover in prokaryotes. We propose that ribosome content is regulated dynamically in eukaryotes by TOR through both ribosome synthesis and the cytoplasmic turnover of mature ribosomes.     

The role of ribosomal ribonucleic acid in the structure and function of mammalian brain ribosomes

In order to resolve the functional role of intact rRNA in polypeptide chain elongation mouse brain ribosomes were treated with dilute pancreatic or T(1) RNAase (ribonuclease). After RNAase treatment, several physical-chemical properties as well as the functional activity of the ribosomes were measured. RNAase treatment resulted in the extensive hydrolysis of both 18S and 28S rRNA; however, the sedimentation properties of mono-ribosomes were unaltered and more than 90% of the relatively low-molecular-weight RNA fragments remained associated with ribosome particles. Analysis of the ability of RNAase-treated ribosomes to participate in cell-free protein synthesis showed that ribosomes with less than 2% intact rRNA retained more than 85% of their activity in polyphenylalanine incorporation. Proof that the incorporation of phenylalanine by ribosomes with hydrolysed rRNA actually represented active translocation was obtained by the effective inhibition of incorporation by diphtheria toxin. In addition, the oligopeptide products of protein synthesis could be identified by BD (benzoylated diethylaminoethyl)-cellulose column chromatography. Analysis of the size distribution of oligopeptides synthesized by normal and RNAase-treated ribosomes showed no significant differences which indicated that there was no change in the proportion of ribosomes engaged in protein synthesis. Thus strong RNA-protein and protein-protein interactions must serve to maintain the functional integrity of ribosomes even when the rRNA is extensively degraded. The ability of the enzyme-treated ribosomes to efficiently incorporate amino acids clearly demonstrated that ;intact' rRNA is not required for protein-synthetic activity.     

On the adjustment of the sex ratio and the gregarious behavior of animal populations.

Ribosome synthesis in bacteria is linked to RNA polymerase synthesis; both synthesis rates depend upon the values of six parameters: (1) fraction of total ribosomes that is functioning, (2) fraction of total RNA polymerase that is functioning, (3) fraction of functioning RNA polymerase engaged in rRNA synthesis, (4) fraction of total protein that is RNA polymerase protein, (5) peptide chain elongation rate, (6) rRNA chain elongation rate. If these parameters are constant in time, then the numbers of both ribosomes and RNA polymerase molecules increase exponentially. It is shown how the rate constant (fractional increase per unit of time) relates to these parameters and how the kinetics of ribosome and RNA polymerase synthesis respond to a change in any of these parameters.     

Effects of ammonium treatment on the protein and chlorophyll contents and the number of ribosomes in Chlamydomonas reinhardtii cells

The effects of exogenous ammonium on total protein and chlorophyll contents and the number of ribosomes in Chlamydomonas reinhardtii (Sager) green alga cells were studied. The absence of ammonium from nutrient medium resulted in a twofold drop in the number of ribosomes in the cytoplasm. The chlorophyll content of the cells grown on ammonium-free nitrate-containing medium insignificantly increased. The increase in the ribosome number in the presence of exogenous ammonium was not accompanied by the elevation of total cellular protein and did not depend on the levels of mRNA of rps6, a small ribosome subunit protein, and the 18S rRNA. Possible reasons for the effect of exogenous ammonium during ribosome biogenesis are discussed.     

Turnover as a control of ribonucleic acid accumulation in bacteria undergoing stepdown.

The synthesis of ribosomes was compared in rel+ and rel- strains of Escherichia coli undergoing "stepdown" in growth from glucose medium to one with lactate as principal carbon source. Two strains (CP78 and CP79), isogenic except for rel, showed similar behaviour with respect to (1) the kinetics of labelling total RNA and ribosomes with exogenous uracil, (2) the proportion of newly formed protein that could be bound with nascent rRNA in mature ribosomes, and (3) the rate of induction of enzymically active beta-galactosidase (relative to the rate of ribosome synthesis). It was concluded that, as there was no net accumulation of RNA during stepdown in either strain, rRNA turnover must be occurring at a high rate. The general features of ribosome maturation in rel+ and rel- cells were almost identical with those found in auxotrophic rel+ organisms starved of required amino acids. In both cases, there was a considerable delay in the maturation of new ribosomal particles, owing to a relative shortfall in the rate of synthesis of ribosome-associated proteins. Only about 4-5% of the total protein labelled during stepdown was capable of binding with newly formed rRNA. This compared with 3.5% for rel+ and 0.5% for rel- auxotrophs during amino acid starvation. The turnover rate for newly formed mRNA and rRNA was virtually the same in "stepped-down" rel+ and rel- strains and was similar to that of the same fraction in amino acid-starved rel+ cells. The functional lifetime of mRNA was also identical. It seems that in the rel- strain many of the characteristics typical of the isogenic rel+ strain are displayed under these conditions, at least as regards the speed of ribosome maturation and the induction of beta-galactosidase. Studies on the thermolability of the latter enzyme induced during stepdown indicate that inaccurate translation, which occurs in rel- strains starved for only a few amino acids, is less evident in this situation than in straightforward amino acid deprivation.     

Comparative analysis of the action of cytokinin and light on the formation of ribulosebisphosphate carboxylase and plastid biogenesis

The role of cytokinin in plastid biogenesis was investigated in etiolated rye leaves (Secale cereale L.) and compared with the effect of white light. Cytokinin deficiency of the leaves was induced by early excision of the seedling roots and reversed by the application of kinetin. The cytokinin supply had a much greater influence on plastid biogenesis than on leaf growth in general. The activities of several chloroplastic enzymes were increased 200%–400% after kinetin treatment of cytokinin-depleted leaves. The activity of ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) and the amount of fraction-I protein even showed a sevenfold increase. In cytokinin-depleted leaves the development of ribulose-1,5-bisphosphate carboxylase and NADP-glyceraldehydephosphate dehydrogenase was specifically, and markedly inhibited by actinomycin D. The inhibition was partially or even completely overcome after treatment with kinetin. However, under all conditions, RNA synthesis of the leaves, was only partially inhibited by actinomycin D. According to immunologic studies, all dark-grown leaves, in addition to the complete enzyme, contained an excess of free small subunit of ribulose-1,5-bisphosphate carboxylase that was absent in mature light-grown leaves. The most striking accumulation of free small subunit, protein occurred in cytokinin-depleted dark-grown leaves, indicating a deficiency of the plastidic synthesis of the large subunit. The capacity as well as the activity of plastidic protein synthesis was preferentially increased by cytokinin and light. Cytokinin increased, the amount of plastidic ribosomes per leaf and relative to the amount of cytoplasmic ribosomes. While the percentage of cytoplasmic ribosomes bound as polyribosomes was little affected by the cytokinin supply, the proportion of plastidic polyribosomes was increased from 11% to 18% after kinetin treatment of cytokinin-depleted leaves. In the light, the proportion of plastidic polyribosomes reached 39% of the total plastidic ribosomes.Abbreviations RuBP carboxylase ribulose-1,5-bisphosphate carboxylase - NADP-GAP dehydrogenase NADP-dependent glyceraldehyde-3-phosphate dehydrogenase     

Effects of Benzylaminopurine and Abscisic Acid on Distribution of rRNA in the Palisade Cells of Excised Cucurbita Pepo Cotyledons

rRNA was labelled with RNase-gold complexes applied to ultrathin Lowicryl sections of excised Cucurbita pepo L. (zucchini) cotyledons grown in darkness. Benzylaminopurine-caused stimulation of cotyledon growth decreases the density of ribosomes in palisade cells despite stimulating rRNA synthesis. Abscisic acid inhibits RNA synthesis and transport, but does not visibly affect the number of pre-existing ribosomes in retarded growth cells. The amount of rRNA in the cells of 24 h treated cotyledons is rather consequence of the growth rate than its leading factor.     

Protein, nucleic acid and starch metabolism in the duckweed Spirodela oligorrhiza, treated with cytokinins

Bacteria-free cultures of Spirodela oligorrhiza continue to increase in frond number for 2 to 3 days after transfer to darkness. There is then no further increase in frond number for 3 to 4 weeks, although DNA, RNA and protein synthesis continue at decreased rates and starch accumulates in the plants. We refer to such ;non-growing' plants in darkness as dormant. Adding kinetin to dormant Spirodela initiated increased DNA, RNA and protein synthesis within 1h, although new fronds were not detected until 24h after the addition of kinetin. The frond number then continued to increase. Starch accumulated in dormant plants. Accumulation of starch appeared to be a consequence of inhibition of growth rather than the converse. No evidence was obtained for a block in [(14)C]glucose metabolism that might explain the lack of growth in darkness in the absence of kinetin. In darkness, more ribosomes were membrane-bound in dormant Spirodela than in Spirodela growing with kinetin. Similarities between the response of Spirodela to darkness, stringent control in bacteria and pleiotypic controls in animal cells are discussed. It is suggested that all three processes are ultimately controlled by specific protein kinases that are individually sensitive to different effectors.     

Effects of serum deprivation, insulin and dexamethasone on polysome percentages in C2C12 myoblasts and differentiating myoblasts.

An increase in the rate of protein synthesis in living cells can be achieved by regulating the quantity of mRNA, ribosomes, and enzymes available for translation or by regulating the efficiency at which existing components are used. Efficiency can be measured by comparing the number of ribosomes actively engaged in the synthesis of protein (polysomes) to the pool of free ribosomes. The objective of this study was to determine the percentage of ribosomes found as polysomes in C2C12 cells deprived of serum or exposed to insulin or dexamethasone 24 h before and after being stimulated to differentiate. Individual 60 mm culture dishes were exposed to serum-free control medium, medium containing serum, insulin, or dexamethasone for a period of 1 h or 2 h and then quickly frozen. The ribosomes and polysomes from these cells were separated by ultracentrifugation on 15 to 60% sucrose gradients and the absorbance across the gradient at 254 nm was recorded. Polysome percentages were determined as the area under the polysome peak divided by the total area under the curve. Serum deprivation caused a 12% decline in the percentage of ribosomes found as polysomes (P < 0.01). Dexamethasone caused a quadratic decline (P < 0.05) in polysome percentage, while insulin yielded a quadratic increase (P < 0.05). Protein synthesis assays measuring 3H-tyrosine uptake showed similar responses. These changes occurred in the absence of any differences in total RNA concentration. It was concluded that differentiation and the absence of serum in the media reduced the rate of recruitment of ribosomes for protein synthesis. Insulin increased ribosome recruitment which was also observed by a similar increase in incorporation of radio-labeled tyrosine.     

Effects of IGF-I, IGF-II, bFGF and PDGF on the initiation of mRNA translation in C2C12 myoblasts and differentiating myoblasts.

In order to study the mechanisms by which growth factors stimulate protein synthesis, C2C12 myogenic cells were treated with a variety of growth factors and the recruitment of free ribosomes to polysomes was quantified. All experiments were conducted on C2C12 myoblasts (24 h prior to induction of fusion) and differentiating myoblasts (24 h after induction of fusion). After the 2 h incubation, cells were rinsed with phosphate buffered saline and quickly frozen at -80 degrees C. Cell lysates were fractionated on 15-60% sucrose gradients by centrifugation at 200,000 x g for 1 h. Absorbance at 254 nm was recorded continuously across the gradient. The response to each of the four growth factors, IGF-I and-II, basic fibroblast growth factor (FGF), and platelet-derived growth factor was a decrease (P < 0.05) in monosome peak height and a increase (P < 0.05) in polysome percentage (P < 0.05). All responses were linear, except IGF-I, and the monosome peak height response to FGF which were quadratic (P < 0.05). None of the growth factors had a significant effect (P > 0.05) on RNA concentrations over the 2-h incubation. Protein content did not vary due to growth factor or level of treatment. This corroborates the hypothesis that the acute increase of protein synthesis exhibited by growth factor treated cells is due to an increase in the activity of existing ribosomes rather than an increase in ribosome synthesis. These results suggest that we can study the mechanisms regulating protein synthesis in muscle cells effectively by studying shifts in ribosomal activity. This method gave more consistent results than the H3-tyrosine incorporation and has the added benefit of not requiring the use of radioactivity. The strong correlation between monosome peak heights and percentage polysomes will allow researchers to measure total protein synthetic activity in a culture from the free or cytoplasmic fraction and to reserve the polysomes for other uses. The similarity of response among the various growth factors may indicate a common mechanism for increasing the initiation of protein synthesis.     

Action of red and far red light on ribosome formation in cabbage seedlings

The action of light on ribosome formation was examined in the cabbage seedlings, a system extensively used in the studies of anthocyanin synthesis. Ribosomes were extracted 18 h after the beginning of the irradiation and separated by sucrose gradient centrifugation. In the cotyledons of dark-grown cabbage seedlings, a brief red light induces an increase both in total ribosomes and in the fraction present as polysomes; the effect of red light is reversed by far red light, indicating the involvement of phytochrome in polysome formation in cabbage seedlings. Continuous red and continuous far red light are about equally effective in bringing about an increase of total ribosomes and of the polysome fraction. Streptomycin, which inhibits chlorophyll synthesis and chloroplast development, and enhances anthocyanin synthesis in cabbage seedlings, causes a decrease of total ribosomes and of the fraction present as polysomes. In hypocotyls, the red-far red reversibility is evident only for the polysome content and streptomycin does not decrease the polysome/monosomo ratio as it does in cotyledons.     

Secondary structure features of ribosomal RNA species within intact ribosomal subunits and efficiency of RNA-protein interactions in thermoacidophilic (Caldariella acidophila, Bacillus acidocaldarius) and mesophilic (Escherichia coli) bacteria

Ribosomal subunits of Caldariella acidophila (max.growth temp., 90 degrees C) have been compared to subunits of Bacillus acidocaldarius (max. growth temp., 70 degrees C) and Escherichia coli (max. growth temp., 47 degrees C) with respect to (a) bihelical content of rRNA; (b) G . C content of bihelical domains and (c) tightness of rRNA-protein interactions. The principal results are as follows. Subunits of C. acidophilia ribosomes (Tm = 90-93 degrees C) exhibit considerable thermal tolerance over their B. acidocaldarius (Tm = 77 degrees C) and E. coli counterparts (Tm = 72 degrees C). Based on the "melting' hyperchromicities of the intact ribosomal subunits a 51-55% fraction of the nucleotides appears to participate in hydrogen-bonded base pairing regardless of ribosome source, whereas a larger fraction, 67-70%, appears to be involved in hydrogen bonding in the naked rRNA species. The G . C content of bihelical domains of both free and ribosome-bound rRNA increases with increasing thermophily; based on hyperchromicity dispersion spectra of intact subunits and free rRNA, the bihelical parts of C. acidophila rRNA are estimated to contain 63-64% G . C, compared to 58.5% G . C for B. acidocaldarius and 55% G . C for E. coli. The increment of ribosome Tm values with increasing thermophily is greater than the increase in Tm for the free rRNA, indicating that within ribosomes bihelical domains of the thermophile rRNA species are stabilized more efficiently than their mesophile counterparts by proteins or/ and other component(s). The efficiency of the rRNA-protein interactions in the mesophile and thermophile ribosomes has been probed by comparing the releases, with LiCl-urea, of the rRNA species from the corresponding ribosomal subunits stuck to a Celite column through their protein moiety; it has been established that the release of C. acidophila rRNA from the Celite-bound ribosomes occurs at salt-urea concentrations about 4-fold higher than those required to release rRNA from Celite-bound E. coli ribosomes. Compared to E. coli the C. acidophila 50 and 30 S ribosomal subunits are considerably less susceptible to treatment designed to promote ribosome unfolding through depletion of magnesium ions.