ON THE ROLE OF AMMONIUM OR POTASSIUM ION IN AMINO ACID POLYMERIZATION

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.

A monovalent cation acts as structural and catalytic cofactor in translational GTPases

Translational GTPases are universally conserved GTP hydrolyzing enzymes, critical for fidelity and speed of ribosomal protein biosynthesis. Despite their central roles, the mechanisms of GTP-dependent conformational switching and GTP hydrolysis that govern the function of trGTPases remain poorly understood. Here, we provide biochemical and high-resolution structural evidence that eIF5B and aEF1A/EF-Tu bound to GTP or GTPγS coordinate a monovalent cation (M(+)) in their active site. Our data reveal that M(+) ions form constitutive components of the catalytic machinery in trGTPases acting as structural cofactor to stabilize the GTP-bound "on" state. Additionally, the M(+) ion provides a positive charge into the active site analogous to the arginine-finger in the Ras-RasGAP system indicating a similar role as catalytic element that stabilizes the transition state of the hydrolysis reaction. In sequence and structure, the coordination shell for the M(+) ion is, with exception of eIF2γ, highly conserved among trGTPases from bacteria to human. We therefore propose a universal mechanism of M(+)-dependent conformational switching and GTP hydrolysis among trGTPases with important consequences for the interpretation of available biochemical and structural data.

Origin of first cells at terrestrial, anoxic geothermal fields

All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the "hatcheries" of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K(+), Zn(2+), Mn(2+), and phosphate. Thus, protocells must have evolved in habitats with a high K(+)/Na(+) ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO(2)-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K(+), Zn(2+), and phosphorous compounds.

Use of natural mRNAs in the cell-free protein-synthesizing systems of the moderate halophile Vibrio costicola

In vitro protein synthesis was studied in extracts of the moderate halophile Vibrio costicola by using as mRNAs the endogenous mRNA of V. costicola and the RNA of the R17 bacteriophage of Escherichia coli. Protein synthesis (amino acid incorporation) was dependent on the messenger, ribosomes, soluble cytoplasmic factors, energy source, and tRNA(FMet) (in the R17 RNA system) and was inhibited by certain antibiotics. These properties indicated de novo protein synthesis. In the V. costicola system directed by R17 RNA, a protein of the same electrophoretic mobility as the major coat protein of the R17 phage was synthesized. Antibiotic action and the response to added tRNA(FMet) showed that protein synthesis in the R17 RNA system, but not in the endogenous messenger system, absolutely depended on initiation. Optimal activity of both systems was observed in 250 to 300 mM NH4+ (as glutamate). Higher salt concentrations, especially those with Cl- as anion, were generally inhibitory. The R17 RNA-directed system was more sensitive to Cl- ions than the endogenous system was. Glycine betaine stimulated both systems and partly overcame the toxic effects of Cl- ions. Both systems required Mg2+, but in lower concentrations than the polyuridylic acid-directed system previously studied. Initiation factors were removed from ribosomes by washing with 3.0 to 3.5 M NH4Cl, concentrations about three times as high as that needed to remove initiation factors from E. coli ribosomes. Washing with 4.0 M NH4Cl damaged V. costicola ribosomes, although the initiation factors still functioned. Cl- ions inhibited the attachment of initiation factors to tRNA(FMet) but had little effect on binding of initiation factors to R17 RNA.

Polypeptide elongation factors of the developing chick brain

The polypeptide elongation factors (EF-1L, EF-1H, and EF-2) of the developing chick brain were separated and purified by means of a combination of gel chromatographic methods. The molecular weight of EF-1H of the chick brain ranged from 5 to 10 x 10(5), and was different from that of the chick liver (about 7 x 10(5). The molecular weight of other purified factors was about 5 x 10(4) for EF-1L and 9.4 x 10(4) for EF-2. High activities of polyphenylalanine (poly-Phe) synthesis per mg protein in the developing chick brain were observed between the 3rd embryonic week and the 1st post-hatch week and declined afterwards. On the other hand, the levels of both EF-1 and EF-2 per mg protein in the brain were observed to be high in an early embryonic stage, gradually declining afterwards to the adult level. The brain EF-1L was a major component of EF-1 in an early embryonic stage, while EF-1H became recognizable in the 3rd embryonic week. Moreover, the EF-1H activities were found to be more than double with regard to the binding reaction and to be more than 10-fold as active in respect to poly-Phe synthesis in comparison with the activities of EF-1L. It is proposed that the brain EF-1H could be due to aggregates consisting of Ef-1L, a stimulatory factor, and other components.

Neural control of gene expression in the skeletal muscle fibre: the nature of the lesion in the muscular protein-synthesizing machinery following denervation

Experiments are reported showing that following 8 days of denervation the function of the protein-synthesizing machinery, operating in the rat gastrocnemius fibres, is altered, probably as a consequence of decreased amounts of ribosomes and actively translated mRNA. In addition, the data obtained show that the amount per muscle and the availability per ribosome of the soluble factors involved in the process of protein synthesis are markedly decreased, thus suggesting that the amounts of ribosomes, mRNA and soluble factors are regulated in a concerted fashion when muscular protein synthesis is decreased after denervation.

Activity coefficients of intracellular Na+ and K+ during development of frog oocytes

The chemical activities, (a), of Na+ and K+ were determined in large mature and in small immature frog oocytes, using open-tipped micropripettes and ion-selective microelectrodes. The average chemical concentrations, c, of Na+ and K+ were determined by spectrophotometry and by electron probe X-ray microanalysis. The apparent activity coefficient (gammaapp) was calculated for each ion as the ratio, a/c. With development, (aNa/ak) decreased four to fivefold and (cNa/cK) increased six to sevenfold. In the large mature oocytes, gammaapp was measured to be 0.08 +/- 0.02 and gammaappK lay within the range 1.15 +/- 0.03 to 1.29 +/- 0.04, constituting the smallest value for Na+ and largest value for K+, respectively, thus far reported. This intracellular value of gammaappK was substantially greater than the activity coefficient of K+ in the external medium (0.76). The data suggest that the inequality of gammaappNa and gammaappK in this and probably other cells reflects the development of subcellular compartmentalization of ions. Possible intracellular sites of ionic compartmentalization are considered.

Protein synthesis in Bacillus subtilis: differential effect of potassium ions on in vitro peptide chain initiation and elongation

The preparation and fractionation of a highly active and stable in vitro protein-synthesizing system from Bacillus subtilis is described. Potassium satisfied the requirement for a monovalent ion when the initiation factor-dependent binding of formyl-methionyl-transfer ribonucleic acid and synthesis of formyl-methionyl-puromycin were assayed, whereas it inhibited the reactions for polyphenylalanine synthesis. On the other hand, the ammonium ion satisfied the requirement for all assayed reactions. The in vitro experimental evidence suggested that potassium is an inhibitor of one or a few specific reactions involved in peptide chain elongation in B. subtilis.

The mechanism of protein synthesis activation after fertilization of sea urchin eggs

Upon fertilization of Paracentrotus lividus eggs, the ability of their ribosomes to form a ternary complex with poly(U) and phenylalanyl-tRNA is enhanced. In addition, it is possible to extract from ribosomes of the unfertilized egg a protein factor that inhibits polyphenylalanine synthesis by decreasing the binding of mRNA and aminoacyl-tRNA to the ribosomes. The observed increase in the rate of protein synthesis that occurs at fertilization could be accounted for by the removal of this inhibitory protein from the ribosomes.

Binding of adenosine 3':5'-cyclic phosphate to G factor of Escherichia coli, and its effects on GTPase, RNase V, and protein synthesis

Unique among adenine nucleotides tested by filter binding assays, 3':5'-cyclic AMP binds to the G translocation factor. Binding is dependent on the presence of GTP, and is inhibited by GDP, by the analog 5'-beta,gamma-methylene GTP, and by the antibiotic fusidic acid. The cAMP seems to be released during the ribosome-dependent translocation of charged tRNA catalyzed by G factor. Bound cAMP inhibits GTPase and ribosome-associated degradation of messenger RNA, but does not inhibit protein synthesis. cAMP might thereby regulate the ratio of productive to degradative transits of ribosomes on messenger RNA, and this may account for some part of its profound effect on levels of specific bacterial messenger RNA species.

Ribonuclease V of escherichia coli. I. Dependence on ribosomes and translocation

A new RNase activity, tentatively named RNase V, was found in cell-free extracts of E. coli. This activity requires ribosomes, G and T factors, tRNA, K(+) or NH(4) (+), Mg(2+), GTP, and a sulfhydryl compound to degrade poly U, poly A, T4 phage mRNA, or E. coli mRNA. RNase V is specific for mRNA; it does not attack ribosomal RNA. It is inhibited by antibiotics that decrease breakdown of mRNA in vivo, such as chloramphenicol and streptomycin, and by such agents as 5'-beta, gamma-methylene-guanosine triphosphate, and fusidic acid, which inhibit ribosome-dependent GTPase and translocation of ribosomes along mRNA. The evidence suggests that RNase V is either an integral part of the ribosome or is tightly associated with it, and that it selectively degrades mRNA in intact cells.

Protein synthetic activity of heart microsomes and robosomes during left ventricular hypertrophy in rabbits

Certain aspects of cytoplasmic protein synthesis have been studied during the early stages (0 to 5 days) of left ventricular hypertrophy produced by supravalvular constriction of the ascending aorta in adult rabbits. At 5 days after constriction, cell-free protein synthesis by microsomal preparations from hypertrophied heart muscle was increased, both from free phenylalanine or leucine (50 to 130%), and from phenylalanyl-soluble RNA, both with (70 to 250%) or without (70 to 150%) polyuridylic acid as artificial messenger. Such increased activity was observed as early as 24 hr, and persisted to 5 days (the limit of the study). Sham preparations also displayed increased activity at 24 hr, which subsided by 5 days. The increased activity could be localized to the microsomal fraction: no differences were found when soluble fractions from normal, sham, and hypertrophied hearts, or from liver, were interchanged. Ribosomes from hypertrophied hearts were no more active than normal ribosomes. Increased yields of microsomal, ribosomal, and soluble RNA were found. It is suggested that the increased protein synthesis occurring in hypertrophy is localized in the microsomes, that soluble factors are not of major significance, and that an increased number of ribosomes (and microsomes) play a major role.