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PubMed2006

Histone modifications: signalling receptors and potential elements of a heritable epigenetic code.

The genetic code epitomises simplicity, near universality and absolute predictive power. By contrast, epigenetic information, in the form of histone modifications, is characterised by complexity, diversity and an overall tendency to respond to changes in genomic function rather than to predict them. Perhaps the transient changes in histone modifications involved in intranuclear signalling and ongoing chromatin functions mask stable, predictive modifications that lie beneath. The current rapid progress in unravelling the diversity and complexity of epigenetic information might eventually reveal an underlying histone or epigenetic code. But whether it does or not, it will certainly provide unprecedented opportunities, both for understanding how the genome responds to environmental and metabolic change and for manipulating its activities for experimental and therapeutic benefit.

Chromatin↗
PubMed2005

Evolution of the genetic triplet code via two types of doublet codons.

Explaining the apparent non-random codon distribution and the nature and number of amino acids in the 'standard' genetic code remains a challenge, despite the various hypotheses so far proposed. In this paper we propose a simple new hypothesis for code evolution involving a progression from singlet to doublet to triplet codons with a reading mechanism that moves three bases each step. We suggest that triplet codons gradually evolved from two types of ambiguous doublet codons, those in which the first two bases of each three-base window were read ('prefix' codons) and those in which the last two bases of each window were read ('suffix' codons). This hypothesis explains multiple features of the genetic code such as the origin of the pattern of four-fold degenerate and two-fold degenerate triplet codons, the origin of its error minimising properties, and why there are only 20 amino acids.

Amino Acids↗
PubMed1997

Four primordial modes of tRNA-synthetase recognition, determined by the (G,C) operational code.

In distinction to single-stranded anticodons built of G, C, A, and U bases, their presumable double-stranded precursors at the first three positions of the acceptor stem are composed almost invariably of G-C and C-G base pairs. Thus, the "second" operational RNA code responsible for correct aminoacylation seems to be a (G,C) code preceding the classic genetic code. Although historically rooted, the two codes were destined to diverge quite early. However, closer inspection revealed that two complementary catalytic domains of class I and class II aminoacyl-tRNA synthetases (aaRSs) multiplied by two, also complementary, G2-C71 and C2-G71 targets in tRNA acceptors, yield four (2 x 2) different modes of recognition. It appears therefore that the core four-column organization of the genetic code, associated with the most conservative central base of anticodons and codons, was in essence predetermined by these four recognition modes of the (G,C) operational code. The general conclusion follows that the genetic code per se looks like a "frozen accident" but only beyond the "2 x 2 = 4" scope. The four primordial modes of tRNA-aaRS recognition are amenable to direct experimental verification.

Amino Acyl-tRNA Synthetases↗
PubMed2003

Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life.

A search has been performed on 2878 tRNA sequences from 60 different genomes in order to detect the existence of closely related 'alloacceptor' tRNAs accepting dissimilar amino acids that could be paralogs generated by gene duplications. This has led to the identification of extremely conserved tRNA(Phe)-tRNA(Tyr) pairs displaying as high as 94% identity between them, and also other potentially paralogous tRNA pairs in archaeal species. These paralogous pairs are enriched for amino acid pairs belonging to the same amino acid biosynthetic family, thus providing evidence for the coevolution of genetic code and amino acid biosynthesis. Overall, the genetic distances between alloacceptor tRNAs yield estimates of how closely clustered in sequence space are the tRNAs in a genome. Among 34 Bacteria, 18 Archaea and 8 Eukarya, Methanopyrus kandleri and Aeropyrum pernix have yielded the lowest alloacceptor distances and largest number of paralogous pairs. Based on a cluster-dispersion model of tRNA evolution, such tight alloacceptor clustering is a measure of primitiveness of tRNA genotypes, and places last universal common ancestor (LUCA) between the branches leading to these two archaea in the tRNA phylogenetic tree.

Amino Acids↗
PubMed1994

Expanding the genetic lexicon: incorporating non-standard amino acids into proteins by ribosome-based synthesis.

Only 20 amino acids are normally incorporated into proteins synthesized in living cells, and this has limited the structural range of proteins that can be prepared. New methods that allow the incorporation of amino acids that are not normally encoded by natural genes are being developed: these include reassigning functions within the existing genetic code, and expanding the genetic code by constructing additional, non-natural codons. Used in conjunction with recent major advances in understanding protein structure-function relationships, these approaches should extend the range of de novo protein designs that are possible.

Amino Acid Sequence↗
PubMed1986

Analysis of the genetic determinants coding for the S-fimbrial adhesin (sfa) in different Escherichia coli strains causing meningitis or urinary tract infections.

Recently we have described the molecular cloning of the genetic determinant coding for the S-fimbrial adhesin (Sfa), a sialic acid-recognizing pilus frequently found among extraintestinal Escherichia coli isolates. Fimbriae from the resulting Sfa+ E. coli K-12 clone were isolated, and an Sfa-specific antiserum was prepared. Western blots indicate that S fimbriae isolated from different uropathogenic and meningitis-associated E. coli strains, including O83:K1 isolates, were serologically related. The Sfa-specific antibodies did not cross-react with P fimbriae, but did cross-react with F1C fimbriae. Furthermore the sfa+ recombinant DNAs and some cloned sfa-flanking regions were used as probes in Southern experiments. Chromosomal DNAs isolated from O18:K1 and O83:K1 meningitis strains with and without S fimbriae and from uropathogenic O6:K+ strains were hybridized against these sfa-specific probes. Only one copy of the sfa determinant was identified on the chromosome of these strains. No sfa-specific sequences were observed on the chromosome of E. coli K-12 strains and an O7:K1 isolate. With the exception of small alterations in the sfa-coding region the genetic determinants for S fimbriae were identical in uropathogenic O6:K+ and meningitis O18:K1 and O83:K1 strains. The sfa determinant was also detected on the chromosome of K1 isolates with an Sfa-negative phenotype, and specific cross-hybridization signals were visible after blotting against F1C-specific DNA. In addition homology among the different strains was observed in the sfa-flanking regions.

Adhesins, Escherichia coli↗
PubMed1996

Transfer RNA structural change is a key element in the reassignment of the CUG codon in Candida albicans.

The human pathogenic yeast Candida albicans and a number of other Candida species translate the standard leucine CUG codon as serine. This is the latest addition to an increasing number of alterations to the standard genetic code which invalidate the theory that the code is frozen and universal. The unexpected finding that some organisms evolved alternative genetic codes raises two important questions: how have these alternative codes evolved and what evolutionary advantages could they create to allow for their selection? To address these questions in the context of serine CUG translation in C.albicans, we have searched for unique structural features in seryl-tRNA(CAG), which translates the leucine CUG codon as serine, and attempted to reconstruct the early stages of this genetic code switch in the closely related yeast species Saccharomyces cerevisiae. We show that a purine at position 33 (G33) in the C.albicans Ser-tRNA(CAG) anticodon loop, which replaces a conserved pyrimidine found in all other tRNAs, is a key structural element in the reassignment of the CUG codon from leucine to serine in that it decreases the decoding efficiency of the tRNA, thereby allowing cells to survive low level serine CUG translation. Expression of this tRNA in S.cerevisiae induces the stress response which allows cells to acquire thermotolerance. We argue that acquisition of thermotolerance may represent a positive selection for this genetic code change by allowing yeasts to adapt to sudden changes in environmental conditions and therefore colonize new ecological niches.

Base Sequence↗
PubMed1998

A genetic testing code of practice for insurers.

The Association of British Insurers has issued a Genetic Testing Code of Practice. The document consists of a forward and six parts, namely; Code of Practice, Statement of Duties of our Insurance Company's Chief Medical Director, Statement of the ABI Genetics advisors responsibilities, Principals of the adjudication system, the legal and ethical framework and confidentiality guidelines.

Genetic Testing↗
PubMed1998

Some traces of hidden codes.

Recent results in comparative genetics reveal processes of neutral evolution that are reminiscent of neutral codon substitutions, although they operate on novel kinds of sequences and molecular structures. This suggests that in addition to the genetic code, previously unrecognized "degenerate" codes might govern molecular interactions at other levels of biological information. If they exist, such multiple degenerate codes cannot be accounted for by the two concepts usually placed at the heart of molecular biology, i.e. molecular cascades and gene networks. This article reports on some representative examples of putative degenerate codes involving three fundamental levels of biological regulation, i.e. transcription, post-transcriptional regulation and signal transduction. From these examples we suggest that degenerate codes are organized hierarchically and that the concept of neutral evolution can be generalized to all kinds of molecular interactions. In addition, a case of functional evolution is interpreted as the emergence of novel, possibly degenerate codes. Comparative genetics and molecular embryology will be instrumental in testing the existence of multiple degenerate codes and hence, in unraveling the causes of evolution.

Animals↗
PubMed1996

UAG is a sense codon in several chlorophycean mitochondria.

The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3-8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined.

Alanine↗
PubMed2003

Evolution of phage with chemically ambiguous proteomes.

BACKGROUND: The widespread introduction of amino acid substitutions into organismal proteomes has occurred during natural evolution, but has been difficult to achieve by directed evolution. The adaptation of the translation apparatus represents one barrier, but the multiple mutations that may be required throughout a proteome in order to accommodate an alternative amino acid or analogue is an even more daunting problem. The evolution of a small bacteriophage proteome to accommodate an unnatural amino acid analogue can provide insights into the number and type of substitutions that individual proteins will require to retain functionality. RESULTS: The bacteriophage Qbeta initially grows poorly in the presence of the amino acid analogue 6-fluorotryptophan. After 25 serial passages, the fitness of the phage on the analogue was substantially increased; there was no loss of fitness when the evolved phage were passaged in the presence of tryptophan. Seven mutations were fixed throughout the phage in two independent lines of descent. None of the mutations changed a tryptophan residue. CONCLUSIONS: A relatively small number of mutations allowed an unnatural amino acid to be functionally incorporated into a highly interdependent set of proteins. These results support the 'ambiguous intermediate' hypothesis for the emergence of divergent genetic codes, in which the adoption of a new genetic code is preceded by the evolution of proteins that can simultaneously accommodate more than one amino acid at a given codon. It may now be possible to direct the evolution of organisms with novel genetic codes using methods that promote ambiguous intermediates.

Allolevivirus↗
PubMed2006

Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice.

The effective number of codons used in a gene is a commonly used measure of codon usage. It varies between 20 and 61 (standard genetic code) and indicates to which degree the entire genetic code is used. It is a drawback of this method that it does not take background composition into account. This led Novembre to introduce a variant called Nc' (Novembre JA. 2002. Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol 19:1390-4). In this letter, its properties are under the loupe, with special emphasis on phenomena relating to codon homozygosity. A theoretical misunderstanding regarding this estimator is explained in detail, notably Nc varies between 0 and 61 instead of 20 and 61 (with the standard genetic code). Practical examples from the genome of Pseudomonas aeruginosa are given which demonstrate that the problem is not just theoretical.

Base Composition↗
PubMed1987

The relationship between the biosynthetic paths to the amino acids and their coding. I: The aliphatic amino acids and proline.

The genetic code could not have been fixed until the means for biosynthesis of the amino acids was at hand. The biosynthetic enzymes could not be optimized until the genetic code ceased to be rearranged. Therefore the development of the code and the development of the biosynthesis of the amino acids occurred concurrently. The present day biosynthetic pathways of amino acids, examined from this point of view, help to explain the present set of coded amino acids, in particular the absence of norvaline, norleucine, homoserine, ornithine, and alpha-aminobutyric acid. An order of development of biosyntheses is also proposed. Lysine was first, followed by valine and isoleucine. The more common primordial amino acids did not need biosyntheses so early. The central pathways of metabolism probably developed in response to a need for amino acid biosynthesis.

Amino Acids↗
PubMed2004

Exploratory studies to investigate a linked prebiotic origin of RNA and coded peptides.

An introduction to the premise that RNA and genetically coded proteins should not be viewed as etiologically discrete entities in the origin of life is presented. This premise follows from the mutual interdependence of RNA and coded proteins in biology and the lack of prebiotically plausible constitutional self-assembly processes leading to either polymeric species. The RNA:coded peptides subsystem and its informational core, the genetic code, are then analysed retrosynthetically to suggest a (replicative) synthesis involving the intermediacy of aminoacyl-RNA trimers (cf. Scheme 5). A number of potential candidate aminoacyl-RNA trimers are identified (23-26; Scheme 6) and a chemical strategy to assess their validity is outlined. Experimental investigation of potential aminoacylation chemistry, nucleobase assembly and phosphate activation rules out three of the trimers but suggests that 26 is worthy of further investigation.

Evolution, Molecular↗
PubMedDate not supplied

[The nature of the genotype and heredity].

The term "genotype" is used for both hereditary information and its substantial bearer. The most important property of the information is relatively of its content which means very weak dependence on properties of the information substantial bearer (genotype of the second meaning) and very strong dependence on properties of the information recipient. Hereditary information (genotype in the first meaning) is addressed to the ontogenesis system, that is, to phenotype. From this it follows: 1) The genotype content is determined not so much by properties of its substantial bearer as by properties of the phenotype to which it is addressed; 2) Certainty of the genotype content depends not so much on stability of its elements, genes, as on stability of the phenotype of adaptive norm; 3) Genotype possess certain content only for a phenotype inherited from the ontogeny of other (maternal) organism or from a previous ontogenetic stage of the same organism; 4) Genotype (and this is true for any hereditary information of an organism) can not be localized in the primary structures of the nucleic acids. It is an aspect of phenotype and not a part thereof and, in this sense, does not possess independent being; 5) Each element of the phenotype, including genotype, relative to its other elements, is both recipient and bearer of hereditary information; 6) Genotype, as genetic code, is specialized but, not the only, "organ" of storing and transferring of hereditary information; 7) There is no two identical genotypes existing in nature; 8) The only operational definition of the genotype is its treating as genetic information localized in one or several loci; 9) Rather strong relation between certain symbols of genetic code (genes) and certain phenotypic characters reflects stability of reactional system of adaptive norm; 10) High semantic university of some symbols of genetic code indicates deep phylogenetic unity of all existing organisms; 11) Biological sense of structural separateness of the genotype within phenotype is creating and supporting of an information pool undestroyable during ontogenetic development; 12) All and only living systems possess reciprocally determining processes of individual and historic development; 13) Heredity, as an ability of descendants to reproduce safely in their ontogeneses the properties of their ancestors is an integral undecomposable (more exactly, decomposable but for operational purposes) property of the life. There is no and could not be any "heredity substance, as there is no and could not be an "information substance".

Animals↗
PubMed1991

Classification of cell receptors.

This manuscript constitutes a first attempt to categorize the cell receptors. Based on evolutionary and biological characteristics, it is possible to classify ligand-receptor units into original families. Certain dynamic patterns that could not be classified previously lead us towards the ligand-receptor unit. Biological information is transformed at the receptor by cellular transduction and effector pathways. The dynamic code is compared with the genetic code. The dynamic code controls the biological information patterns necessary for the integral function and structure of cells, tissue, organs, and organisms. The genetic code controls the assembly and molecular structure of proteins. The original families can be assigned certain original functions. A coevolution of ligand-receptor and dynamic code is revealed. For the time being the most useful approach to receptor classification would seem to be based on the organization of the molecular and protein structure of receptors. Two classes of receptor can be described: receptors for cyclic hydrophobic compounds and membrane receptors. Until we know of the families of single membrane-spanning receptors, fourfold membrane-spanning receptors, sevenfold membrane-spanning receptors, fourfold membrane-spanning receptors. For the sevenfold membrane-spanning receptor the identity of conformation and dynamics of biological function has been established. Light and peptide ligands are used as examples. A systems theory for information transduction at receptors is introduced which can also describe the processes of sensitivity modulation.

Amino Acid Sequence↗