Initiating protein synthesis with noncanonical amino acids in vivo using an engineered orthogonal initiator tRNA

Author(s):  
Jeffery M. Tharp
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fan Liu ◽  
Siniša Bratulić ◽  
Alan Costello ◽  
Teemu P. Miettinen ◽  
Ahmed H. Badran

AbstractIn bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo.


1972 ◽  
Vol 54 (2) ◽  
pp. 279-294 ◽  
Author(s):  
David C. Shephard ◽  
Wendy B. Levin

The ability of chloroplasts isolated from Acetabulana mediterranea to synthesize the protein amino acids has been investigated. When this chloroplast isolate was presented with 14CO2 for periods of 6–8 hr, tracer was found in essentially all amino acid species of their hydrolyzed protein Phenylalanine labeling was not detected, probably due to technical problems, and hydroxyproline labeling was not tested for The incorporation of 14CO2 into the amino acids is driven by light and, as indicated by the amount of radioactivity lost during ninhydrin decarboxylation on the chromatograms, the amino acids appear to be uniformly labeled. The amino acid labeling pattern of the isolate is similar to that found in plastids labeled with 14CO2 in vivo. The chloroplast isolate did not utilize detectable amounts of externally supplied amino acids in light or, with added adenosine triphosphate (ATP), in darkness. It is concluded that these chloroplasts are a tight cytoplasmic compartment that is independent in supplying the amino acids used for its own protein synthesis. These results are discussed in terms of the role of contaminants in the observed synthesis, the "normalcy" of Acetabularia chloroplasts, the synthetic pathways for amino acids in plastids, and the implications of these observations for cell compartmentation and chloroplast autonomy.


1973 ◽  
Vol 51 (12) ◽  
pp. 933-941 ◽  
Author(s):  
Njanoor Narayanan ◽  
Jacob Eapen

The effect of cycloheximide in vitro and in vivo on the incorporation of labelled amino acids into protein by muscles, liver, kidneys, and brain of rats and pigeons was studied. In vitro incorporation of amino acids into protein by muscle microsomes, myofibrils, and myofibrillar ribosomes was not affected by cycloheximide. In contrast, administration of the antibiotic into intact animals at a concentration of 1 mg/kg body weight resulted in considerable inhibition of amino acid incorporation into protein by muscles, liver, kidneys, and brain. This inhibition was observed in all the subcellular fractions of these tissues during a period of 10–40 min after the administration of the precursor. Tissue homogenates derived from in vivo cycloheximide-treated animals did not show significant alteration in in vitro amino acid incorporation with the exception of brain, which showed a small but significant enhancement.


1971 ◽  
Vol 122 (3) ◽  
pp. 267-276 ◽  
Author(s):  
D. C. N. Earl ◽  
Susan T. Hindley

1. At 3 min after an intravenous injection of radioactive amino acids into the rat, the bulk of radioactivity associated with liver polyribosomes can be interpreted as growing peptides. 2. In an attempt to identify the rate-limiting step of protein synthesis in vivo and in vitro, use was made of the action of puromycin at 0°C, in releasing growing peptides only from the donor site, to study the distribution of growing peptides between the donor and acceptor sites. 3. Evidence is presented that all growing peptides in a population of liver polyribosomes labelled in vivo are similarly distributed between the donor and acceptor sites, and that the proportion released by puromycin is not an artifact of methodology. 4. The proportion released by puromycin is about 50% for both liver and muscle polyribosomes labelled in vivo, suggesting that neither the availability nor binding of aminoacyl-tRNA nor peptide bond synthesis nor translocation can limit the rate of protein synthesis in vivo. Attempts to alter this by starvation, hypophysectomy, growth hormone, alloxan, insulin and partial hepatectomy were unsuccessful. 5. Growing peptides on liver polyribosomes labelled in a cell-free system in vitro or by incubating hemidiaphragms in vitro were largely in the donor site, suggesting that either the availability or binding of aminoacyl-tRNA, or peptide bond synthesis, must be rate limiting in vitro and that the rate-limiting step differs from that in vivo. 6. Neither in vivo nor in the hemidiaphragm system in vitro was a correlation found between the proportion of growing peptides in the donor site and changes in the rate of incorporation of radioactivity into protein. This could indicate that the intracellular concentration of amino acids or aminoacyl-tRNA limits the rate of protein synthesis and that the increased incorporation results from a rise to a higher but still suboptimum concentration.


1971 ◽  
Vol 124 (2) ◽  
pp. 385-392 ◽  
Author(s):  
R. W. Wannemacher ◽  
C. F. Wannemacher ◽  
M. B. Yatvin

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.


1995 ◽  
Vol 14 ◽  
pp. 20
Author(s):  
R. Barazzoni ◽  
M. Zanetti ◽  
M. Vettore ◽  
S. Normand ◽  
D. Bruttomesso ◽  
...  

1968 ◽  
Vol 109 (1) ◽  
pp. 87-91 ◽  
Author(s):  
S. Villa-Treviño ◽  
D. D. Leaver

1. Aflatoxin and the pyrrolizidine alkaloid retrorsine inhibited the incorporation of labelled amino acids into rat liver and plasma proteins in vivo. Inhibition was greater and detected earlier with retrorsine (1hr.) than with aflatoxin (3hr.). 2. Both toxins affected the liver ribosomal aggregates, causing increases in the proportion of monomers plus dimers. The effect of retrorsine was greater than that of aflatoxin. 3. Incorporation of labelled amino acids into proteins of cell-free preparations of liver from rats treated with aflatoxin was lower than in control preparations. The main site of inhibition appeared to be the ribosomes. 4. Both toxins inhibited the incorporation of orotate into liver nuclear RNA 1hr. after administration.


1976 ◽  
Vol 231 (2) ◽  
pp. 441-448 ◽  
Author(s):  
JB Li ◽  
AL Goldberg

The effects of food deprivation on protein turnover in rat soleus and extensor digitorum longus (EDL) were investigated. Muscles were removed from fed or fasted growing rats, and protein synthesis and breakdown were measured during incubation in vitro. Rates of synthesis and degradation were higher in the dark soleus than in the pale EDL. One day after food removal protein synthesis and RNA content in the EDL decreased. On the 2nd day of fasting, rates of protein catabolism in this muscle increased. Little or no change in synthesis and degradation occurred in the soleus. Consequently, during fasting the soleus lost much less weight than the EDL and other rat muscles. In unsupplemented buffer or in medium containing amino acids, glucose, and insulin, the muscles of fasted rats showed a lower rate of protein synthesis expressed per milligram of tissue but not per microgram of RNA. Thus the decrease in muscle RNA on fasting was responsible for the reduced synthesis observed under controlled in vitro conditions. In vivo the reduction in muscle protein synthesis on fasting results both from a lower RNA content and lower rate of synthesis per microgram of RNA. Reduced supply of glucose, insulin, and amino acids may account for the lower rate of synthesis per microgram of RNA demonstrable in vivo.


1987 ◽  
Vol 241 (2) ◽  
pp. 491-498 ◽  
Author(s):  
D Pérez-Sala ◽  
R Parrilla ◽  
M S Ayuso

We investigated the effects of administration of single amino acids to starved rats on the regulation of protein synthesis in the liver. Of all the amino acids tested, only alanine, ornithine and proline promoted statistically significant increases in the extent of hepatic polyribosome aggregation. The most effective of these was alanine, whose effect of promoting polyribosomal aggregation was accompanied by a decrease in the polypeptide-chain elongation time. The following observations indicate that alanine plays an important physiological role in the regulation of hepatic protein synthesis. Alanine was the amino acid showing the largest decrease in hepatic content in the transition from high (fed) to low (starved) rates of protein synthesis. The administration of glucose or pyruvate is also effective in increasing liver protein synthesis in starved rats, and their effects were accompanied by an increased hepatic alanine content. An increase in hepatic ornithine content does not lead to an increased protein synthesis, unless it is accompanied by an increase of alanine. The effect of alanine is observed either in vivo, in rats pretreated with cycloserine to prevent its transamination, or in isolated liver cells under conditions in which its metabolic transformation is fully impeded.


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