The concept of the intracellular amino acid pool and its relevance in the regulation of protein metabolism, with particular reference to mammalian cells

Natural history and experimental evolution of the genetic code

The standard genetic code is a set of rules that relates the 20 canonical amino acids in proteins to groups of three bases in the mRNA. It evolved from a more primitive form and the attempts to reconstruct its natural history are based on its present-day features. Genetic code engineering as a new research field was developed independently in a few laboratories during the last 15 years. The main intention is to re-program protein synthesis by expanding the coding capacities of the genetic code via re-assignment of specific codons to un-natural amino acids. This article focuses on the question as to which extent hypothetical scenarios that led to codon re-assignments during the evolution of the genetic code are relevant for its further evolution in the laboratory. Current attempts to engineer the genetic code are reviewed with reference to theoretical works on its natural history. Integration of the theoretical considerations into experimental concepts will bring us closer to designer cells with target-engineered genetic codes that should open not only tremendous possibilities for the biotechnology of the twenty-first century but will also provide a basis for the design of novel life forms.

Arginine deprivation and metabolomics: important aspects of intermediary metabolism in relation to the differential sensitivity of normal and tumour cells

Arginine deprivation causes many types of tumour cells to die, often because they cannot recover or convert urea cycle intermediates into arginine. The powerful homeostatic mechanisms that kicks in to restore arginine levels in vivo are lacking in vitro, where there is no supply of citrulline. Comparison between cells deprived of arginine by direct elimination methods or indirectly via arginine degrading enzymes should show differences depending on their ability to handle alternative intermediates (ornithine, citrulline and argininosuccinate) of the urea cycle. The internal state of cells that can, versus those that cannot, use intermediates will metabolically be quite different. These differences should provide clear indicators regarding the sensitivity (susceptibility) of cells to arginine deprivation, from which we will be in a much better position to judge which tumours to treat, and possibly how to design the best treatment to eliminate them.

Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire

Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.

Growth during the cell cycle

During the cell cycle, major bulk parameters such as volume, dry mass, total protein, and total RNA double and such growth is a fundamental property of the cell cycle. The patterns of growth in volume and total protein or RNA provide an "envelope" that contains and may restrict the gear wheels. The main parameters of cell cycle growth were established in the earlier work when people moved from this field to the reductionist approaches of molecular biology, but very little is known on the patterns of metabolism. Most of the bulk properties of cells show a continuous increase during the cell cycle, although the exact pattern of this increase may vary. Since the earliest days, there have been two popular models, based on an exponential increase and linear increase. In the first, there is no sharp change in the rate of increase through the cycle but a smooth increase by a factor of two. In the second, the rate of increase stays constant through much of the cycle but it doubles sharply at a rate change point (RCP). It is thought that the exponential increase is caused by the steady growth of ribosome numbers and the linear pattern is caused by a doubling of the structural genes during the S period giving an RCP--a "gene dosage" effect. In budding yeast, there are experiments fitting both models but on balance slightly favoring "gene dosage." In fission yeast, there is no good evidence of exponential increase. All the bulk properties, except O2 consumption, appear to follow linear patterns with an RCP during the short S period. In addition, there is in wild-type cells a minor RCP in G2 where the rate increases by 70%. In mammalian cells, there is good but not extensive evidence of exponential increase. In Escherichia coli, exponential increase appears to be the pattern. There are two important points: First, some proteins do not show peaks of periodic synthesis. If they show patterns of exponential increase both they and the total protein pattern will not be cell cycle regulated. However, if the total protein pattern is not exponential, then a majority of the individual proteins will be so regulated. If this majority pattern is linear, then it can be detected from rate measurements on total protein. However, it would be much harder at the level of individual proteins where the methods are at present not sensitive enough to detect a rate change by a factor of two. At a simple level, it is only the exponential increase that is not cell cycle regulated in a synchronous culture. The existence of a "size control" is well known and the control has been studied for a long time, but it has been remarkably resistant to molecular analysis. The attainment of a critical size triggers the periodic events of the cycle such as the S period and mitosis. This control acts as a homeostatic effector that maintains a constant "average" cell size at division through successive cycles in a growing culture. It is a vital link coordinating cell growth with periodic events of the cycle. A size control is present in all the systems and appears to operate near the start of S or of mitosis when the cell has reached a critical size, but the molecular mechanism by which size is measured remains both obscure and a challenge. A simple version might be for the cell to detect a critical concentration of a gene product.

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Chirality differences in amino acid retention and release from acid-extractable pool of cultured mammalian cells

In previous work, no chiral differences were found between D and L enantiomers of Leu in their ability to displace one another from the acid-extractable pool in mammalian cells. Recent evidence suggested otherwise. Our aim is to examine whether, in physiological range, D-amino acids have an equivalent ability to displace L-amino acids from the acid-extractable pool of HeLa cells, and vice versa. In the Millimolar range, D-Leu and L-Leu have similar uptake and displacement properties with regard to the acid-extractable pool in HeLa cells, despite only the latter isomer being incorporated into protein. Below millimolar concentration however, a distinct difference was found in the displacement of tritium-labelled L-Leu from the pool by unlabelled D-Leu compared with unlabelled L-Leu. Thus, unlabelled L-Leu in the external medium at 10(-4) or 10(-5) M displaced and equivalent amount of label from the pool ad D-Leu introduced at a concentration approx. one order of magnitude higher, respectively. Reciprocal experiments, in which the acid-extractable pool was preloaded with 3H-D-Leu, confirmed this finding. The chirality difference was noted whether pool prelabelling was carried out at 37 or 0 degrees C; but in order to avoid the complications of active transport mechanisms, the competition work reported here was done at 0 degrees C. Similar chirality differences were observed with other hydrophobic amino acids, including His, Ile, and Phe, such as, preferential displacement by the L-Leu racemer compared with the D-Leu racemer below mM levels. This was also true for the D and L forms of the non-utilisable isomer of Leu, norleucine (nLeu). We conclude that D-forms of hydrophobic amino acids have lower affinity for similar or the same intracellular binding sites involved in the acid-extractable pool than in their L-forms. The significance of these findings to amino acid pools in cells, and to the predominance of L-forms of amino acids in the biosphere is considered

Subcellular distribution of selenium in deficient mouse liver

Selenium (Se)-deficient mice were labelled in vivo with single pulses of [75Se]selenite, and the intrahepatic distribution of the trace element was studied by subcellular fractionation. At 1 h after intraperitoneal injection of 3.3 or 10 micrograms of Se/kg body weight, 15% of the respective doses were found in the liver. Accumulation in the subcellular fractions followed the order: Golgi vesicular much greater than lysosomal greater than cytosolic = microsomal greater than mitochondrial, peroxisomal, nuclear and plasma-membrane fraction. At a dose of 3.3 micrograms/kg, more than 90% of the hepatic Se was protein-bound. When cross-contamination was accounted for, the following specific Se contents of the subcellular compartments were extrapolated: Golgi apparatus, 7.50 pmol/mg; cytosol, 0.90 pmol/mg; endoplasmic reticulum, 0.80 pmol/mg; mitochondria, 0.49 pmol/mg; nuclei, lysosomes, peroxisomes and plasma membrane, less than 0.4 pmol/mg. At 10 micrograms/kg, a roughly 2-3-fold increase in Se content of all fractions was found without major changes in the intrahepatic distribution pattern. An extraordinary rise in the cytosolic fraction was due to an apparently non-protein-bound Se pool. At 24 h after dosing, total hepatic Se had decreased to 6% of the initial dose and had become predominantly protein-bound. The 60% decrease in hepatic Se was reflected in a similar fall in the subcellular levels of the trace element. The Golgi apparatus still had the highest specific Se content, although accumulation was 5 times less than that after 1 h. The cytosolic pool accounted for 50% of the hepatic Se at both labelling times. After 1 h the Golgi apparatus was, with 19%, the second largest intrahepatic pool, followed by the endoplasmic reticulum with 16%. The high affinity and fast response of the Golgi apparatus to Se supplementation of deficient mice is interpreted in terms of a predominant function of this cell compartment in the processing and the export of Se-proteins from the liver.

L-929 cells under hyperosmotic conditions. Water, Na+, and K+

Changes in cell water content resulting from sorbitol addition to the environment of L-929 cells were evaluated gravimetrically using 14C-labeled polyethylene glycol as a probe of extracellular space. Reductions in cell water were proportional to sorbitol supplements up to 0.6 molal, above which no further measurable decrease occurred. No volume regulation occurred for at least 1 h but the percentage of cell water lost was quickly regained when physiological conditions were restored. The amount of cell water lost because of a given hyperosmotic exposure was found to exceed the loss of cell volume. That discrepancy could be the result of an overestimation of extracellular space and/or an underestimation of cell volume reduction as a result of in-folding of the cell surface. Na+ and K+ were also measured in cells of variable water content and volume: no significant change occurred in the amounts of these ions per cell, but large increases in total cell concentration resulted from hyperosmotic exposure. The sum of Na+ and K+ concentrations exceeds the total osmotic pressure of the medium indicating that an appreciable fraction of Na+ and K+ must be bound to fixed charges within the cells. The results are evaluated in the context of intracellular organization.