Protein synthesis in the early stages of cardiac hypertrophy

Cardiac hypertrophy, induced in rats by either tri-iodothyronine or isoproterenol, administered daily for 7 days, was monitored using several parameters. Both treatments increased RNA concentrations 24 hr after the first injection, while heart weight increased following 2 injections to 46% above control after 7 days. Cardiac protein synthetic activity, as determined by the rate of peptidyl-puromycin formation, was increased by both tri-iodothyronine and isoproterenol 24 hr after a single injection, implying an increase in the number of functional ribosomes. RNA activity (the rate of peptidyl-puromycin formation per unit RNA) remained constant, suggesting that neither accelerated rates of initiation or translation nor increased activation of pre-existing, non-translating ribosomes was involved in the observed increase in protein synthetic activity. In contrast, constant infusion of [14C] tyrosine indicated no change in protein synthetic rate 24 hr after a single tri-iodothyronine injection and decreased protein synthetic rate after isoproterenol injection. It is concluded that the use of [3H]puromycin to estimate protein synthetic activity may be a more sensitive procedure for detecting early changes in protein synthesis in cardiac hypertrophy than constant isotope infusion, owing to the problems associated with determining the precise precursor pool for protein synthesis in this latter method.     

Effect of food deprivation and hypophysectomy on in vitro protein synthesis by membrain-bound and free hepatic ribosomes.

The protein synthetic activities of membrane-bound and free hepatic ribosomes isolated from intact rats fed ad libitum, and normal rats subjected to food restriction to match that of hypophysectomised (Hx) rats were compared to the in vitro protein synthetic capacity of hepatic ribosomes isolated from Hx rats. Hypophysectomy resulted in decreased protein synthetic ability of bound ribosomes, whether protein synthesis was directed by endogenous messenger RNA (mRNA) (p less than 0.05) or by polyuridylic acid (polyU) (p less than 0.01). In contrast, the protein synthetic activity of free hepatic ribosomes from Hx rats was reduced when protein synthesis was directed by endogenous mRNA (p less than 0.05) but, when polyU was substituted as the messenger, the protein synthetic activity of these free ribosomes was equal to that of control rats. On the other hand the effects of food restriction on hepatic ribosomal function could be clearly differentiated from the effects observed following hypophysectomy. Thus, the reduced protein synthetic activity of hepatic bound ribosomes isolated from food restricted normal rats was not demonstrable, when polyU was used to direct protein synthesis. Further, food restriction had no effect on the protein synthetic activity of free hepatic ribosomes, and this was true when protein synthesis was directed by either endogenous or artificial messenger. It is concluded that hypophysectomy reduces the protein synthetic ability of both bound and free hepatic ribosomes, and this change of ribosomal function of Hx rats cannot be attributed to their decreased food intake.     

Mechanism of cell contact-dependent glycolipid synthesis: further studies with glycolipid-glass complex

An initiation factor from rabbit reticulocytes can overcome the block in initiation of protein synthesis occurring in reticulocyte lysates when exogenous hemin is not present, or when double-stranded RNA is added. This factor has been identified with IF-MP, an initiation factor capable of forming ternary complexes with GTP and methionyl-tRNA_F. Initiation factor IF-M3 by itself is unable to overcome the block in initiation, but appears to stimulate this activity of IF-MP. IF-MP binds to single-stranded R17 RNA as well as to double-stranded RNA, while IF-M3 only binds to double-stranded RNA. The protein synthetic activity of IF-MP is sensitive to N-ethylmaleimide, but its ability to bind RNA is resistant.     

RNase PH catalyzes a synthetic reaction, the addition of nucleotides to the 3' end of RNA.

Escherichia coli RNase PH is a phosphate-dependent exoribonuclease that has been implicated in the 3' processing of tRNA precursors. It degrades RNA chains in a phosphorolytic manner releasing nucleoside diphosphates as products. Here we show that RNase PH also catalyzes a synthetic reaction, the addition of nucleotides to the 3' termini of RNA molecules. The synthetic activity co-purifies with RNase PH throughout an extensive enrichment indicating that it is due to the same enzyme. The synthetic activity can incorporate all nucleoside diphosphates, but not triphosphates, and is strongly inhibited by Pi, but not PPi. Various RNA molecules stimulate nucleotide incorporation, and with tRNA the 3' end of the molecule serves a primer function. RNA chains as long as 40 residues can be synthesized in this system. As with polynucleotide phosphorylase, the synthetic activity of RNase PH apparently represents the reversal of the degradative reaction.     

Nucleolin promotes secondary structure in ribosomal RNA

The effect of nucleolin on the secondary structure of RNA was studied using circular dichroism (CD). Nucleolin caused decreases in the main positive bands and shifts to higher wavelengths in the CD spectra of synthetic polynucleotides such as poly(G) and poly(A) indicating helix destabilizing activity. In contrast, nucleolin effected increases in signal and shifts to lower wavelengths of the peaks of CD spectra of ribosomal RNA, suggesting enhancement of secondary structure. Another major nucleolar RNA binding protein, B23, had helix destabilizing activity but did not enhance RNA secondary structure. It is proposed that nucleolin promotes formation of secondary structure in preribosomal RNA during the early stages of ribosome biogenesis.     

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.     

Regulation of protein activity with small-molecule-controlled inteins

Inteins are the protein analogs of self-splicing RNA introns, as they post-translationally excise themselves from a variety of protein hosts. Intein insertion abolishes, in general, the activity of its host protein, which is subsequently restored upon intein excision. These protein elements therefore have the potential to be used as general molecular "switches" for the control of arbitrary target proteins. Based on rational design, an intein-based protein switch has been constructed whose splicing activity is conditionally triggered in vivo by the presence of thyroid hormone or synthetic analogs. This modified intein was used in Escherichia coli to demonstrate that a number of different proteins can be inactivated by intein insertion and then reactivated by the addition of thyroid hormone via ligand-induced splicing. This conditional activation was also found to occur in a dose-dependent manner. Rational protein engineering was then combined with genetic selection to evolve an additional intein whose activity is controlled by the presence of synthetic estrogen ligands. The ability to regulate protein function post-translationally through the use of ligand-controlled intein splicing will most likely find applications in metabolic engineering, drug discovery and delivery, biosensing, molecular computation, as well as many additional areas of biotechnology.     

Purification and partial characterization of megamodulin, a heat-stable protein factor from E. coli and its stimulatory effect on RNA polymerase holoenzyme

Megamodulin, a heat-stable protein from Escherichia coli was isolated and purified near homogeneity as determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis. It had a molecular weight of 71,000 and pl between 3.5 and 4.0. This factor stimulated E. coli RNA polymerase 71-fold in the presence of a synthetic template such as poly (rA).p(dT). When TATAAA sequence was used as template, the RNA polymerase activity was increased 68 times by this factor. The possible mechanism by which this protein factor may regulate the RNA polymerase activity has been described.     

Enzymatic synthesis of a 21-nucleotide coat protein binding fragment of R17 ribonucleic acid

An oligoribonucleotide with a sequence identical with the bacteriophage R17 replicase initiator region has been synthesized. The sequence also encompasses the binding domain of R17 coat protein, which is known to act as a translational repressor at this site. The 21-nucleotide fragment was synthesized entirely by enzymatic methods, T4 RNA ligase being used to join shorter oligomers. The resulting fragment has a secondary structure with the expected thermal stability. Since the synthetic fragment binds R17 coat protein with the same affinity as a 59-nucleotide fragment isolated from R17 RNA, we conclude that it has full biological activity.     

Effect of riboflavin on monoamine oxidase activity in cultured neuroblastoma cells

Monoamine oxidase (MAO) depends on a covalently attached FAD cofactor for activity. Activity is depressed in mouse neuroblastoma cells (NIE-115) grown in synthetic N2 medium lacking riboflavin. MAO activity in depleted cells is stimulated by added riboflavin, and this recovery is blocked by inhibitors of RNA and protein synthesis, and not by an inhibitor of protein glycosylation. Recovery from riboflavin depletion appears to depend upon new RNA and protein synthesis, and not on the addition of FAD cofactor to an inactive MAO precursor.     

Multiple Enzymatic Activities Associated with Recombinant NS3 Protein of Hepatitis C Virus

The hepatitis C virus (HCV) nonstructural 3 protein (NS3) contains at least two domains associated with multiple enzymatic activities; a serine protease activity resides in the N-terminal one-third of the protein, whereas RNA helicase activity and RNA-stimulated nucleoside triphosphatase activity are associated with the C-terminal portion. To study the possible mutual influence of these enzymatic activities, a full-length NS3 polypeptide of 67 kDa was expressed as a nonfusion protein in Escherichia coli, purified to homogeneity, and shown to retain all three enzymatic activities. The protease activity of the full-length NS3 was strongly dependent on the activation by a synthetic peptide spanning the central hydrophobic core of the NS4A cofactor. Once complexed with the NS4A-derived peptide, the full-length NS3 protein and the isolated N-terminal protease domain cleaved synthetic peptide substrates with comparable efficiency. We show that, as in the case of the isolated protease domain, the protease activity of full-length NS3 undergoes inhibition by the N-terminal cleavage products of substrate peptides corresponding to the NS4A-NS4B and NS5A-NS5B. We have also characterized and quantified the NS3 ATPase, RNA helicase, and RNA-binding activities under optimized reaction conditions. Compared with the isolated N-terminal and C-terminal domains, recombinant full-length NS3 did not show significant differences in the three enzymatic activities analyzed in independent in vitro assays. We have further explored the possible interdependence of the NS3 N-terminal and C-terminal domains by analyzing the effect of polynucleotides on the modulation of all NS3 enzymatic functions. Our results demonstrated that the observed inhibition of the NS3 proteolytic activity by single-stranded RNA is mediated by direct interaction with the protease domain rather than with the helicase RNA-binding domain.     

Decreased synthetic activity as a possible cause of the death of Escherichia coli bacteria during amino acid starvation

The work is concerned with studying the breakdown of proteins and RNA when a polyauxotrophic Escherichia coli strain is incubated in a salt solution without amino acids, phosphorus, nitrogen and glucose at 43 degrees C as well as the ability of starving bacterial cells to recommence protein and RNA synthesis (also in the course of phage T4 infection) and to reproduce bacteriophages T4, lambda and MS2. Within the first two hours of the incubation, 12% of proteins and 40% of RNA break down to acid-soluble fragments. Then protein degradation stops while RNA decomposition goes on, but at a lower rate. Within 4-6 h of starvation, the rate of protein and RNA synthesis drops down 4-5 times and the survival rate equals 40-60% when the cells are transferred onto a complete medium. The quantitative characteristics of phages T4, lambda and MS2 reproduction fall down in prestarved cells. The authors speculate that E. coli cells die off in the course of starvation not because some unique structure is destroyed, but owing to the fact that the activity of enzymes and ribosomes gradually declines. As a result, the synthetic activity of the cell drops down abruptly and irreversibly because the enzymes are inactivated and RNA breaks down, which eventually causes cell death.     

Designing and using RNA scaffolds to assemble proteins in vivo

RNA scaffolds are synthetic noncoding RNA molecules with engineered 3D folding harnessed to spatially organize proteins in vivo. Here we provide a protocol to design, express and characterize RNA scaffolds and their cognate proteins within 1 month. The RNA scaffold designs described here are based on either monomeric or multimeric units harboring RNA aptamers as protein docking sites. The scaffolds and proteins are cloned into inducible plasmids and expressed to form functional assemblies. RNA scaffolds find applications in many fields in which in vivo organization of biomolecules is of interest. RNA scaffolds provide extended flexibility compared with DNA or protein scaffolding strategies through programmed modulation of multiple protein stoichiometry and numbers, as well as the proteins' relative distances and spatial orientations. For synthetic biology, RNA scaffolds provide a new platform that can be used to increase yields of sequential metabolic pathways.     

Kinetics of messenger accumulation coding for IFN gamma, related to modifications in the poly(A) RNA population of activated human lymphocytes.

Exposure of human lymphocytes to a mitogen induces the appearance of newly synthesized RNAs and proteins. This study describes the changes in overall synthesis as measured by pulse labelling of PHA treated lymphocytes as well as a qualitative analysis of the protein synthetic patterns "in vivo" and "in vitro". Both the levels of RNA and protein synthesis increase drastically in PHA stimulated cells, while cultures incubated without mitogen remained at background levels. The low translational activity in control cells is not due to the absence of messengers since the extracted RNAs clearly direct the synthesis of high molecular weight proteins when translated "in vitro". A number of qualitative differences are seen in the "in vitro" translation of RNA extracted from induced and non-induced lymphocytes, although the apparent protein synthetic pattern "in vivo" remains identical. The secretion of IFN- gamma is one of the newly expressed functions in stimulated lymphocytes and therefore has been studied more detailed in a time-course of the messenger level compared to the secreted activity of the medium. A specific probe was used to quantitate in Northern blot's the accumulation of mRNA coding for IFN- gamma.     

A mutation in helicase motif III of E. coli RecG protein abolishes branch migration of Holliday junctions.

The RecG protein of Escherichia coli catalyses branch migration of Holliday junctions made by RecA and dissociates synthetic X junctions into duplex products in reactions that require hydrolysis of ATP. To investigate the mode of action of this enzyme a chromosomal mutation that inactivates recG (recG162) was cloned and sequenced. The recG162 mutation is a G:C to A:T transition, which produces an Ala428 to Val substitution in the protein. This change affects a motif (motif III) in the protein that is highly conserved in DNA and RNA helicases. RecG162 protein was purified and shown to retain the ability to bind synthetic X and Y junctions. However, it does not dissociate these junctions and fails to catalyse branch migration of Holliday junction intermediates purified from a RecA strand exchange reaction. RecG162 retains a DNA-dependent ATPase activity, but this is much reduced relative to the wild-type protein, especially with single-stranded DNA as a co-factor. These results suggest that branch migration by RecG is related to a junction-targeted DNA helicase activity.     

Characterization of RNA synthesized during germination of Blastocladia ramosa zoospores

The synthesis of RNA was studied during the synchronous germination of Blastocladia ramosa zoospores. Comparison of RNA synthesis during germination of B. ramosa and Blastocladiella emersonii zoospores revealed that B. ramosa has a longer lag time before RNA synthesis is initiated and, in addition, the rate of RNA synthesis is ten-fold lower in B. ramosa. Zoospores of B. ramosa were shown to contain pre-formed messenger RNA but this messenger RNA directs only a portion of the protein synthesis which occurs during early germination. The conclusion that the remainder of the protein synthetic activity of the germinating spores is due to new message synthesis was supported by demonstrating that the timing of the initation of protein synthesis on new messages correlates with the time RNA synthesis is initiated. New message synthesis was also demonstrated by the incorporation of label into RNA which contains a poly (A) fragment. Synthesis of all classes of RNA including ribosomal, messenger, and transfer RNA was shown to be initiated at the same time. The implications of this observation are discussed.     

Sequence of molecular events involved in induction of allophanate hydrolase.

Addition of urea to an uninduced culture of Saccharomyces at 22 C results in appearance of allophanate hydrolase activity after a lag of 12 min. We have previously demonstrated that both ribonucleic acid (RNA) and protein synthesis are needed for this induction to occur. To elucidate the time intervals occupied by known processes involved in induction, temperature-sensitive mutants defective in messenger RNA transport from nucleus to cytoplasm (rna1) and in protein synthesis initiation (prt1) were employed along with an RNA polymerase inhibitor in experiments that measure cumulative synthetic capacity to produce allophanate hydrolase. These measurements identify the time within the lag period at which each of the above processes is completed. We observed that RNA synthesis, rna1 gene product function, and protein synthesis initiation are completed at 1 to 1.5, 4, and 9 to 10 min, respectively.