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At least 991 records · Page 55Linked to original sources
PubMed1992

Protein synthesis in Aspergillus nidulans.

In this review of protein synthesis, we have described a system for translation of mRNA using extracts of A. nidulans. This system is useful for characterizing mutants suspected to have defects in protein synthesis and for assessing the toxicity of various antibiotics and their effects on misreading the genetic code. The well developed genetical system of A. nidulans has enabled us to map at least 27 new genes whose mutation disturbs the level of translational accuracy. These mutants could be used to identify new components of translation or new roles for established components. The abundant fidelity mutations themselves could be used to elucidate the mechanism for maintaining the accuracy of protein synthesis. The large number of mutations in the control of fidelity indicate that mutations in other parts of the translation system could be easily obtained. This would be particularly important for initiation where many factors are thought to be needed and yet their exact roles are unknown. A. nidulans appears to have normal eukaryotic ribosomes and translation factors that can be used to study the mechanism of protein synthesis, its regulation, and the maintenance of its high fidelity. If highly purified factors were used, requirements for hitherto undiscovered factors could be seen. Since A. nidulans has typical eukaryotic responses to inhibitors of translation, it could be used to study new inhibitors, their mode of action, and their potency. Among the fungi, A. nidulans could be a worthy competitor to S. cerevisiae in the field of protein synthesis, particularly because so many translation genes have been identified. The system awaits further exploitation.

Aspergillus nidulans↗
PubMed1993

[The genetic language: grammar, semantics, evolution].

The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering.

Codon↗
PubMed1995

On the statistical distribution of amino acid residue in randomly synthesized peptides.

The probability of randomly synthesized peptides having an excess of a given residue Ri (nRi > N/2; N = size of the peptide) decreases strongly with peptide size. For a strong specific interaction of a Ri, rich peptide with a given sequence of a ribotide chain, peptides should be reasonably large. We discuss how a compromise can be achieved that may have had an important role on the origin of the genetic code.

Amino Acids↗
PubMedDate not supplied

[Convergent origin of repeats in genes coding for globular proteins. An analysis of the factors determining the presence of inverted and symmetrical repeats].

The factors, determining the presence of inverted and symmetrical repeats in genes coding for globular proteins, have been analysed. An interesting property of genetical code has been revealed in the analysis of symmetrical repeats: the pairs of symmetrical codons corresponded to pairs of amino acids with mostly similar physical-chemical parameters. This property may explain the presence of symmetrical repeats and palindromes only in genes coding for beta-structural proteins-polypeptides, where amino acids with similar physical-chemical properties occupy symmetrical positions. A stochastic model of evolution of polynucleotide sequences has been used for analysis of inverted repeats. The modelling demonstrated that only limiting of sequences (uneven frequencies of used codons) is enough for arising of nonrandom inverted repeats in genes.

Amino Acid Sequence↗
PubMed1999

Characterization and comparison of Escherichia coli transfer RNAs by graph theory based on secondary structure.

We have developed a model to characterize the tRNA structures of Escherichia coli using graph theory. First of all, tRNAs were represented as graphs, whose vertices correspond to nucleotides and the edges to phosphodiester and hydrogen bond linkages. Vertices and edges were weighted using the results of a preliminary quantum study of the nucleotides and the possible coupling between pair bases using the semiempirical method AM1. For each vertex, we defined a nucleotide valence that measures the capability of forming hydrogen bonds. Edges were differentiated by using bond orders. We have proposed weighted structural descriptors-closely related to molecular Randic connectivity and Balaban distance indices-as a distinctive characteristic of each structure. Molecules were characterized by a set of weighted structural descriptors and classified by a clustering method and discriminant function analysis. Two main groups of tRNAs that correspond to the biosynthetic amino acid pathways, in agreement with Wong's coevolution theory of the genetic code, were obtained.

Escherichia coli↗
PubMed1994

The non-enzymatic specific amino-acylation of transfer RNA at high pressure.

This paper shows that the phenylalanine-specific tRNA of Escherichia coli as well as the yellow lupin methionine initiator tRNAMet can be charged specifically with phenylalanine and methionine, respectively, in the absence of specific aminoacyl-tRNA synthetases, under high pressure of a maximum of 6 kbar (1 bar = 10(5) Pa; 1 atm = 1.01 x 10(5) Pa). The esterification reaction takes places at the 3' end of the tRNA molecules. The yield of Phe-tRNAPhe or Met-tRNAMet at high pressure is approximately 10 times lower than that of the enzymatic aminoacylation reaction. This reaction seems to be specific, and mis-aminoacylation of tRNAPhe and tRNAMet with serine is negligible. It is well known that tRNA undergoes conformational changes during interaction with an aminoacyl-tRNA synthetase. Similarly, on the basis of circular dichroism spectra, we showed that the conformation of tRNA at high pressure differs slightly from its original A-RNA form. Therefore, it can be speculated that the chargeable conformation of tRNA induced by the aminoacyl-tRNA synthetase during enzymatic aminoacylation and the one created at high pressure are similar and are most probably formed by a dehydration mechanism. We think that the 'unique' tertiary structure of tRNA existing under high pressure creates an active centre which might itself catalyse ester bond formation. Therefore, the structure of the amino acid stem of tRNA may determine (code) the charging of the particular amino acid to specific tRNA. This code is clearly distinct from the rules of the classical genetic code.

Acylation↗
PubMed1990

Amino acid complementarity: testing of hypotheses.

To determine whether hypotheses about the complementarity of amino acids based on the genetic code reflect the amino acid contact preferences found in natural proteins, the average contact probabilities for hypothetical complementary amino acid pairs were compared with those for all possible remaining pairs of the corresponding subset. A statistically significant preference was found for contact between amino acids with codons which had the same central nucleotide. Conversely, the contact probabilities for amino acids with complementary codons either did not exceed, or exceeded only insignificantly, the value for the corresponding remainder subset. The data obtained do not support the hypothesis for the complementarity of peptides coded by complementary RNA strands.

Amino Acids↗
PubMed2006

A molecular model for the origin of protein translation in an RNA world.

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). A model for this, based on the core of the large subunit of the ribosome, is developed further. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have "poisoned" the ribopolymerase by cross-reacting with the nucleoside triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of amino-acylated tRNA-like products. Using base-pairing interactions, it is suggested that some of these molecules might cross-link two ribopolymerases giving rise to a precursor of the modern ribosome with two subunits linked by tRNA. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors. Some implications for the genetic code are discussed.

Animals↗
PubMed1981

[Optimization against the occurrence of terminators for theoretical doublet codes].

The aim of this work is the study of the internal laws of logic of the genetic code. If we accept, as a major hypothesis, selection against the occurrence of terminators, this leads us to the optimisation of theoretical code resistance to non sense effects. Depending on how the notion of vocabulary extension is envisaged, several methods exist. One of them is presented here for the simplest doublet codes.

Base Composition↗
PubMed2004

Selection on codon usage for error minimization at the protein level.

Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based on amino acid similarity. This measure is used to calculate the degree of error minimization for 82 genes of Drosophila melanogaster and 432 rodent genes and to study its relationship with CG content, the degree of codon usage bias, and the rate of nucleotide substitution. I show that (i) Drosophila and rodent genes tend to prefer codons that minimize errors; (ii) this cannot be merely the effect of mutation bias; (iii) the degree of error minimization is correlated with the degree of codon usage bias; (iv) the amino acids that contribute more to codon usage bias are the ones for which synonymous codons differ more in the capacity to minimize errors; and (v) the degree of error minimization is correlated with the rate of nonsynonymous substitution. These results suggest that natural selection for error minimization at the protein level plays a role in the evolution of coding sequences in Drosophila and rodents.

Amino Acids↗
PubMed2005

Do universal codon-usage patterns minimize the effects of mutation and translation error?

BACKGROUND: Do species use codons that reduce the impact of errors in translation or replication? The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon. However, the extent to which organisms optimize the genetic messages written in this code has been far less studied. We tested whether codon and amino-acid usages from 457 bacteria, 264 eukaryotes, and 33 archaea minimize errors compared to random usages, and whether changes in genome G+C content influence these error values. RESULTS: We tested the hypotheses that organisms choose their codon usage to minimize errors, and that the large observed variation in G+C content in coding sequences, but the low variation in G+U or G+A content, is due to differences in the effects of variation along these axes on the error value. Surprisingly, the biological distribution of error values has far lower variance than randomized error values, but error values of actual codon and amino-acid usages are actually greater than would be expected by chance. CONCLUSION: These unexpected findings suggest that selection against translation error has not produced codon or amino-acid usages that minimize the effects of errors, and that even messages with very different nucleotide compositions somehow maintain a relatively constant error value. They raise the question: why do all known organisms use highly error-minimizing genetic codes, but fail to minimize the errors in the mRNA messages they encode?

Animals↗