The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA

The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the past ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.     

Evolution of the genetic code.

Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.     

On the information content of the genetic code

In living organisms 20 amino acids along with the terminator value(s) are encoded by 64 codons giving a degeneracy of the codons as described by the genetic code. A basic theoretical problem of genetic codes is to explain the particular distribution of degeneracies of partitions involved in the codes. In this work the degeneracy problem is considered in the framework of information theory. It is shown by direct numerical evaluation of a certain degeneracy information function associated with the genetic code that the degeneracy of the codes is observed to be related to the optimization of this function.     

Amino-acid content of leguminous proteins as affected by genetic and nutritional factors. II

Summary Quantitative analyses have been carried out on air-dried plant material in respect of the amino-acid composition as a function of condition of cultivation and selection of variety. Arginine occurs in both the varieties of clover examined and not, as was earlier reported on the basis of the paper chromatographic analysis, only in the tetraploid variety.No pronouced differences between inoculated and non-inoculated plants or between genetically different clovers were demonstrated. The total nitrogen content was higher in the inoculated plants.     

Amino acid content of leguminous proteins as affected by genetic and nutritional factors III

Summary Pea proteins have been extracted from ground peas, and albumin, vicilin and legumin have been isolated. The electrophoretic homogenity of the proteins was tested by means of free electrophoresis and the amino acid composition was determined by column chromatography.     

Evolution of a genetic code simulated with the computer

A simple selforganizing model system of molecules is considered and it is demonstrated by a computer simulation, that a genetic code of 16 elements (aminoacids) can gradually be formed by such a system in the course of many generations. By a number of rare chance events, each suppressing other events of equal a priori probability, a single code results out of an immense number of possible codes of the same a priori probability. The result is discussed in relation to the uniqueness of the genetic code in living systems. The computer simulation emphasizes a particular step in a model pathway discussed elsewhere consisting of many assumed physicochemical steps leading to a genetic apparatus.     

Evolution of mitochondrial genomes and the genetic code.

Mitochondrial genomes are clearly marked by a strong tendency towards reductive evolution. This tendency has been facilitated by the transfer of most of the essential genes for mitochondrial propogation and function to the nuclear genome. The most extreme examples of genomic simplification are seen in animal mitochondria, where there also are the greatest tendencies to codon reassignment. The reassignment of codons to amino acids different from those designated in the so called universal code is seen in part as an expression of the reduction of the number of genes used by these genomes to code for tRNA species. The driving force for the reductive evolution of mitochondrial genomes is identified with two population genetic effects which may also be operating on populations of parasites.     

Amino acid content of leguminous proteins as affected by genetic and nutritional factors. I.

Summary Tetraploid and diploid red clover have been cultivated in greenhouse under aseptic conditions. The plant cultures were given only one source of nitrogen: either they were given nitrate in the nutrient solution or they were inoculated withRhizobium for establishing symbiotic fixation.The amino acid composition of protein from the different series and from different parts of the plants was analysed by paper chromatography.There was a clear arginine reaction from the tetraploid clover material but no arginine at all was found in the diploid clover material.Plants fed on nitrate and those fed on symbiotically fixed nitrogen showed the same amino acid pattern as far as can be judged from the chromatograms. The hydrolysates from inoculated plants showed usually more intense ninhydrine reaction on the chromatograms than hydrolysates from not inoculated plants, although diluted to the same nitrogen content. For this fact we have so far no explanation.     

Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

With an analysis of the structural constraints of the anticodon-codon interaction within the decoding center of the ribosome, we show that the extent of degeneracy at the third position of the anticodon is determined by the level of stability of the base pair at the second position.     

Glycolate oxidase content of microbodies as affected by nitrate

Glycolate oxidase is loosely held by microbodies obtained from etiolated barley (Hordeum vulgare L.) leaves depleted of nitrate. Defined centrifugation conditions cause the complete detachment of the enzyme from the microbodies. Addition of nitrate to these plants brings about a greater retention of glycolate oxidase by the microbodies. Synthesis of a nitrate-induced protein seems to be responsible for the enhanced retention of glycolate oxidase. Catalase, on the contrary, is strongly attached to the microbodies under all nutritional and experimental conditions considered.     

Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code

The aminoacyl-tRNA synthetases exist as two enzyme families which were apparently generated by divergent evolution from two primordial synthetases. The two classes of enzymes exhibit intriguing familial relationships, in that they are distributed nonrandomly within the codon-amino acid matrix of the genetic code. For example, all XCX codons code for amino acids handled by class II synthetases, and all but one of the XUX codons code for amino acids handled by class I synthetases. One interpretation of these patterns is that the synthetases coevolved with the genetic code. The more likely explanation, however, is that the synthetases evolved in the context of an already-established genetic code—a code which developed earlier in an RNA world. The rules which governed the development of the genetic code, and led to certain patterns in the coding catalog between codons and amino acids, would also have governed the subsequent evolution of the synthetases in the context of a fixed code, leading to patterns in synthetase distribution such as those observed. These rules are (1) conservative evolution of amino acid and adapter binding sites and (2) minimization of the disruptive effects on protein structure caused by codon meaning changes.     

Cyclic AMP content of autonomic ganglia as affected by catecholamines

The relative content of cAMP was measured in the rat ganglion nodosum, lumbar ganglia of the sympathetic trunk, the main pelvic ganglion and intramural ganglia of the heart. It was observed that the basal level of cAMP in the cardiac ganglia was lower than in other ganglia. The process of stimulation of the cAMP content by noradrenaline was most pronounced in the main pelvic and lumbar ganglia, that by dopamine in the cardiac ganglia. The catecholamines failed to alter the cAMP content in the ganglion nodosum.     

Enzyme content of plant microbodies as affected by experimental procedures

The content of specific enzymes in microbodies isolated from tobacco Nicotiana rustica, L. leaves may vary according to the procedure followed during the isolation of the organelles. The type of homogenizing medium, its ionic components and the ratio of medium to tissue during homogenization, affect the over-all yield and relative distribution of each microbody enzyme in different ways. The type of density gradient and the initial acceleration of the centrifuge rotor affect also the enzyme content of sedimenting microbodies. These observations explain some of the conflicting results obtained on the determination of the intracellular location of several enzymes.     

Evolution of the mitochondrial genetic code IV. AAA as an asparagine codon in some animal mitochondria

Summary Differences in assignments from those in the universal genetic code occur in codes of mitochondria. In this report, the published sequences of the mitochondrial genes for COI and ND1 in a platyhelminth (Fasciola hepatica) are examined and it is concluded that AAA may be a codon for asparagine instead of lysine, whereas AAG is the sole codon for lysine in this species.     

The impact of including tRNA content on the optimality of the genetic code

Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, since it is known that, when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The relative gene copy frequencies of tRNAs are used as estimates of the tRNA content. We also altered the rule previously used for the calculation of the probabilities of single base mutation occurrences. Our model signifies higher optimality of the genetic code towards load minimization and suggests the presence of a coevolution of tRNA frequency and the genetic code.     

The genetic code as a periodic table

Summary The contemporary genetic code is reflective of a significant correlation between the properties of amino acids and their anticodons in a periodic manner. Almost all properties of amino acids showed a greater correlation to anticodonic than to codonic dinucleoside monophosphate properties. The polarity and bulkiness of amino acid side chains can be used to predict the anticodon with considerable confidence. The results are most consistent with predictions of the direct interaction and ambiguity reduction hypotheses for the origin of the genetic code.     

The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria

It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that the anticodon is GPsiU, U35 at the anticodon second position being modified to pseudouridine (Psi). In contrast, mt tRNALys, corresponding to another lysine codon, AAG, has the anticodon CUU. mt tRNAs possessing anti-codons closely related to that of tRNAAsn, but responsible for decoding only two codons each-tRNAHis, tRNAAsp and tRNATyr-were found to possess unmodified U35 in all cases, suggesting the importance of Psi35 for decoding the three codons. Therefore, the decoding capabilities of two synthetic Escherichia coli tRNAAla variants with the anticodon GPsiU or GUU were examined using an E.coli in vitro translation system. Both tRNAs could translate not only AAC and AAU with similar efficiency, but also AAA with an efficiency that was approximately 2-fold higher in the case of tRNAAlaGPsiU than tRNAAlaGUU. These findings imply that Psi35 of echinoderm mt tRNAAsn actually serves to decode the unusual asparagine codon AAA, resulting in the alteration of the genetic code in echinoderm mitochondria.     

Phosphorus content and growth of fenugreek as affected by cadmium application

Changes in growth and phosphorus content in plants and seeds of fenugreek with increasing cadmium concentration was evaluated. Root length and shoot length ranged from 11.63 to 27.72 and from 9.70 to 54.78 cm, respectively. With the increasing Cd²⁺ concentration there was a significant decrease in root and shoot length, and fresh mass. Various phosphorus fractions of shoot decreased with increasing Cd²⁺ concentration except lipid P and nucleic acid P which increased at 65 and 95 d after sowing and protein P only increased at vegetative stage. In seeds (60 d after flowering) lipid P increased except at 2.5 μg(Cd²⁺) g^?1 (soil) while protein P decreased.