Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic code”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,495 records · Page 83Linked to original sources
PubMed1998

Enhanced vasorelaxation by overexpression of beta 2-adrenergic receptors in large arteries.

This study was designed to determine if adenoviral-mediated delivery of a transgene encoding the beta 2-adrenergic receptor (beta 2-AR) to the carotid arterial wall could result in alterations in in vivo vascular function. De-endothelialized rat carotid arteries were infused in vivo with 0.1 mg/ml elastase and adenovirus [6 x 10(9) plaque forming units (PFU)] containing either the marker gene beta-galactosidase (Adeno-beta-gal), DNA encoding the human beta 2-AR (Adeno-beta 2-AR), or no transgene. This low concentration of elastase increased the water permeability (5.2 +/- 0.6 v 1.9 +/- 0.4 x 10(-8) cm/s/mmHg, n = 4, P < 0.0001) without affecting either the vasomotor responsiveness or the morphology of the arterial wall. A transfection efficiency of 73% was achieved with Adeno-beta-gal (n = 3). beta-gal expression was associated with infrequent appearance of T and B lymphocytes, or neutrophil infiltration. Five days after infection with Adeno-beta 2-AR, the total beta-AR density increased six-fold (67.8 +/- 3.4 v 397.0 +/- 155.5 fmol/mg protein, n = 5, P < 0.01); isoproterenol-induced vasorelaxation at transmural pressures from 10-110/mmHg increased (P < 0.01) compared to arteries exposed to control virus (empty adenovirus), n = 4; and isoproterenol-stimulated cAMP production was increased by 65% (n = 5). Thus, adenoviral-mediated delivery of beta 2-ARs into large artery walls results in enhanced beta-AR-mediated vasorelaxation via augmentation in cAMP levels in vascular smooth muscle cells.

Adenoviridae↗
PubMed1993

A joint prediction of the folding types of 1490 human proteins from their genetic codons.

The codon usages for 1490 human proteins have been published by Wada et al. (1990). Based on these data, the frequencies of occurrence of 20 amino acids for each of the 1490 proteins have been calculated according to the genetic codes. Proteins are generally classified into five folding types, i.e. the alpha, beta, alpha + beta, alpha/beta and zeta (irregular) types. The folding type of a protein is correlated to its amino acid composition. By means of three methods established by different investigators, the folding type for each of the 1490 human proteins has been predicted. It has been demonstrated that the accuracy of prediction for the 1490 human proteins is at least 80% by examining the predicted results of some structurally known proteins with these methods. There are only six proteins for which there is uncertainty about their folding types as completely inconsistent results were obtained when predicted with the three different methods. For the remaining 1484 human proteins the numbers of alpha, beta, alpha + beta, alpha/beta, and zeta folding type proteins were found to be 128, 235, 169, 933 and 19, respectively, suggesting that the alpha/beta type proteins would predominate in this set of human proteins. The occurrence frequencies of bases in the first, second and third codon position for each folding type of protein have been calculated. It is shown that the folding type of a protein is strongly dependent on the ratio of frequency of base G in the first codon position with that in the second codon position. The biological implication of the results has been discussed.

Amino Acid Sequence↗
PubMed1993

Simulation studies of self-replicating oligoribotides, with a proposal for the transition to a peptide-assisted stage.

A two-substrate Michaelis-Menten mechanism previously proposed for the self-replication of RNA-like oligomers is developed. Differential growth depends on the existence of two pairs of complementary monomers and leads to 2n groups of 2n components each (n is the oligomer size). As n increases the 2n groups tend to overlap with one another, and the efficiency of the process to increase the information content of the strands decreases. In a second stage we suppose that randomly synthesized peptides with one predominant amino acid interacted with the ribotides, increasing the growth rate of some of them, and at the same time had their mean life increased by interactions with other ribotides of the same kinetic group. Natural selection could have preserved a favourable codon-anticodon-amino acid correlation, the precursor of the modern genetic code.

Animals↗
PubMed1995

Were RNA replication and translation directly coupled in the RNA (+protein?) World?

The ribosome is proposed to have evolved from an ancestor that simultaneously replicated and translated template RNA. At its decoding site, this ancestor to the ribosome carried a ribozyme that assembled product RNA by sequentially ligating anticodon triplets excised from tRNAs. This ribozyme was the ancestor of the Group I introns, which are still present on some ribosomal RNA precursors. Coupling of reversible RNA replication by transesterification with the thermodynamically favourable process of transpeptidation provides a rationale for the evolution of the complete ribosome as a replicase for large RNAs in the RNA (+protein?) world. A detailed and experimentally verifiable mechanism can be proposed for simultaneous replication and translation. Sequence requirements for recognition of the decoding complex as a substrate helix by these ribozymes are consistent with earlier models for the origin of the genetic code, but require an indirect mode for ribosomal self-replication. This proposal has the potential to explain the location of Group I introns in the anticodon loops of some tRNAs.

Animals↗
PubMed1998

Nonlinear Variation in Simulated Complex Pattern Development.

Simulated spore walls manufactured from colloidal polystyrene latex, cyclohexane and water demonstrate a range of structure comparable with that occurring within the walls of Selaginella megaspores. Initial investigation of the relationship between the initiation parameters of the self-assembling simulation and its ultimate structure imply a nonlinear relationship. It is suggested that such self-assembly processes result in structure that cannot be directly mapped onto an equivalent genetic coding and that phylogenetic analyses based on self-assembled structure may differ in its conclusions from that based on DNA sequences.Copyright 1998 Academic Press Limited

Journal Article↗
PubMed1999

The non-monophyletic origin of the tRNA molecule.

The hypothesis that the tRNA molecule may have originated from the assembly of two similar RNA hairpin structures is utilised to understand the evolutionary period in which this molecule originated. Consistent with the exon theory of genes is the observation that the introns in tRNA genes are found almost exclusively in the anticodon loop and "stitched together" the two halves of the molecule, which originally may have been simply two hairpin structures and which can still be observed in the three-dimensional structure of tRNAs. This theory therefore considers these hairpin structures as minigenes on which complex protein synthesis may have been achieved. This in turn leads to the belief that the organisation of the genetic code may have been determined by use of the hairpin structures but not the complete tRNA molecule. In view of this, it can be conjectured that tRNA molecules might have been assembled only after the establishment of the main phyletic lines. If this is all true, then the origin of the tRNA molecule might have been non-monophyletic, i.e. a tRNA specific for a certain amino acid might have been assembled in different phyletic lines with a second and different hairpin structure. This leads to the belief that tRNAs specific for different amino acids but belonging to the same phyletic line might have been more similar to one another than to tRNAs specific for the same amino acid but belonging to different phyletic lines. This prediction seems to be supported by phylogenetic analysis making major use of the bootstrap technique performed on the tRNA sequences and by analysis already existing in the literature which supports the non-monophyletic origin of the tRNA molecule. The main conclusion of this paper is that if the tRNA molecule was assembled in the main phyletic lines this would imply a still rapidly evolving translation apparatus which, in turn, seems to imply that the last universal common ancestor was a progenote.

Amino Acids↗
PubMed2001

Ribosomal crystallography: from poorly diffracting microcrystals to high-resolution structures.

The cellular organelles translating the genetic code into proteins, the ribosomes, are large, asymmetric, flexible, and unstable ribonucleoprotein assemblies, hence they are difficult to crystallize. Despite two decades of intensive effort and thorough searches for suitable sources, so far only three crystal types have yielded high-resolution structures: two large subunits (from an archaean and from a mesophilic eubacterium) and one thermophilic small subunit. These structures have added to our understanding of decoding, have revealed dynamic aspects of the biosynthetic process, and have indicated the strategies adopted by ribosomes for interacting between themselves as well as with inhibitors, factors and substrates.

Archaea↗
PubMed1994

Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex.

RAP30 and RAP74 are subunits of RAP30/74 (TFIIF, beta gamma), a general initiation and elongation factor for transcription by RNA polymerase II. Methods were previously published for production of human RAP30 and RAP74 in bacterial cells, using a bacteriophage T7 promoter expression system. The vectors described for production of RAP74 were not very efficient and produced significant quantities of RAP74 amino terminal fragments. To improve these vectors, a segment of the human RAP74 cDNA was recoded using a preferred set of codons for translation in Escherichia coli. Recoding dramatically improved protein production and suppressed production of amino-terminal fragments. Improved vectors are reported that produce RAP74 with an LEHHHHHH carboxy-terminal extension (RAP74-H6), for purification on a Ni(2+)-affinity column, and also with the native carboxy terminus (RAP74). Methods for purification of RAP74-H6 and RAP74 are reported. Using these improved vectors, approximately 30 mg of soluble and active RAP74-H6 or RAP74 can be produced and purified from 1 liter of E. coli culture, representing a 10-fold improvement in protein production. Methods have also been developed for reconstitution of native RAP30/74 complex using recombinant proteins. This complex has indistinguishable activity from human RAP30/74 for accurate transcription in vitro.

Amino Acid Sequence↗
PubMed1999

Multiple mitochondrial viruses in an isolate of the Dutch Elm disease fungus Ophiostoma novo-ulmi.

The nucleotide sequences of three mitochondrial virus double-stranded (ds) RNAs, RNA-4 (2599 nucleotides), RNA-5 (2474 nucleotides), and RNA-6 (2343 nucleotides), in a diseased isolate Log1/3-8d2 (Ld) of the Dutch elm disease fungus Ophiostoma novo-ulmi have been determined. All these RNAs are A-U-rich (71-73% A + U residues). Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive-strand of each of RNAs 4, 5, and 6 contains a single open reading frame (ORF) with the potential to encode a protein of 783, 729, and 695 amino acids, respectively, all of which contain conserved motifs characteristic of RNA-dependent RNA polymerases (RdRps). Sequence comparisons showed that these RNAs are related to each other and to a previously characterized RNA, RNA-3a, from the same O. novo-ulmi isolate, especially within the RdRp-like motifs. However, the overall RNA nucleotide and RdRp amino acid sequence identities were relatively low (43-55% and 20-32%, respectively). The 5'- and 3'-terminal sequences of these RNAs are different, but they can all be folded into potentially stable stem-loop structures. Those of RNA-4 and RNA-6 have inverted complementarity, potentially forming panhandle structures. Their molecular and biological properties indicate that RNAs 3a, 4, 5, and 6 are the genomes of four different viruses, which replicate independently in the same cell. These four viruses are also related to a mitochondrial RNA virus from another fungus, Cryphonectria parasitica, recently designated the type species of the Mitovirus genus of the Narnaviridae family, and to a virus from the fungus Rhizoctonia solani. It is proposed that the four O. novo-ulmi mitochondrial viruses are assigned to the Mitovirus genus and designated O. novo-ulmi mitovirus (OnuMV) 3a-Ld, 4-Ld, 5-Ld, and 6-Ld, respectively. Northern blot analysis indicated that O. novo-ulmi Ld nucleic acid extracts contain more single-stranded (ss, positive-stranded) RNA than dsRNA for all three newly described mitoviruses. O. novo-ulmi RNA-7, previously believed to be a satellite-like RNA, is shown to be a defective RNA, derived from OnuMV4-Ld RNA by multiple internal deletions. OnuMV4-Ld is therefore the helper virus for the replication of both RNA-7 and another defective RNA, RNA-10. Sequence comparisons indicate that RNA-10 could be derived from RNA-7, as previously suggested, or derived directly from RNA-4.

3' Untranslated Regions↗
PubMed2001

Animal lectins: from initial description to elaborated structural and functional classification.

The genetic code connects the two biochemical dimensions of nucleic acids and proteins. Theoretical calculations on coding capacity reveal that oligosaccharides as hardware surpass peptides by more than seven orders of magnitude based on hexamer synthesis. Thus, the sugar code establishes the third dimension of biological information transfer. Using carbohydrate-binding proteins (lectins, enzymes and antibodies) the information content of such epitopes is decoded. Currently, five families of animal lectins are defined in structural terms. i.e. the C-type, I-type and P-type groups, the galectins and the pentraxins. They are involved in intra- and intercellular glycan routing using oligosaccharides as postal-code equivalents and acting as defense molecules homing in on foreign or aberrant glycosignatures, as crosslinking agent in biosignaling and as coordinator of transient or firm cell-cell/cell-matrix contacts. By delineating the driving forces toward complex formation, knowledge about the causes for specificity can be turned into design of custom-made high-affinity ligands for clinical application, e.g. in anti-adhesion therapy, drug targeting or diagnostic histopathology.

Animals↗
PubMed1983

Computer applications in recombinant DNA research.

I have tried to describe why the computer is an essential tool for the recombinant DNA scientist. As our data bases grow, we will require information storage and communication systems unlike the paper based record systems with which we currently work. Molecular biological data is being generated so rapidly that I believe electronic data exchange will soon be the only way we will be able to keep each other up to date. We have seen some specific computer applications which provide assistance to the researcher at the bench. Sequence manipulation, analysis, and display are too difficult for the unaided molecular biologist to accomplish readily. The computer, being able to provide intelligence at speeds unmatchable by humans, will continue to be used as a tool in recombinant DNA research and will rapidly grow to be an essential tool for all scientists.

Amino Acid Sequence↗
PubMed2000

The alkylated thiohydantoin method for C-terminal sequence analysis.

The alkylated-thiohydantoin method for C-terminal sequencing makes a significant improvement to the thiohydantoin method first described by Schlack and Kumpf. Prior to cleavage from the protein, the C-terminal thiohydantoin is alkylated, making it a better leaving group than the unmodified thiohydantoin. The C-terminal alkylated-thiohydantoin can be cleaved from the protein under conditions that simultaneously form the next thiohydantoin. Combining cleavage and thiohydantoin formation in one step eliminates the need for activating the C-terminal carboxyl group before every sequencing cycle and prevents detection of C-termini formed by random cleavage of peptide bonds in the protein during the sequencing chemistry. The alkylated-thiohydantoin method includes the presequencing modification of cysteine and lysine and the automated modification of aspartic and glutamic acids, serine and threonine. Modifying the reactive side-chain groups improves the ability to sequence through and detect these amino acids. The alkylated-thiohydantoin method can sequence through and detect 19 of the 20 genetically coded amino acids. Sequencing stops at proline residues.

Alkylation↗
PubMed1998

Biosynthesis of D-amino acid-containing peptides: exploring the role of peptide isomerases.

The discovery of D-amino acid residues in a growing number of gene-encoded peptides suggests that such biochemical modifications are more common than initially thought. In fact, the extent to which D-amino acids are incorporated into peptides by multicellular organisms probably has not been fully realized, since routine Edman sequencing does not provide the absolute stereochemistry of amino acid residues. Unless both the D and L isomers of a particular peptide sequence are isolated, D-amino acid-containing peptides are often identified only after synthesis of naturally-occurring peptide fails to yield the desired activity. To date, D-amino acid residues (e.g., alanine, methionine, leucine, isoleucine, phenyl alanine, asparagine, tryptophan and serine) have been identified in peptides from a variety of species, including frogs, snails, clams, lobsters and spiders. While most have a single D-amino acid residue located near their N-termini, an exception is found with omega-Aga IVB. The examples highlighted in this chapter are the result of a unique strategy of multicellular organisms to circumvent stereochemical limitations imposed by the genetic code in an effort to increase molecular diversity. The presence of D-amino acids permits the generation of novel tertiary structure that could not be accessed from L-amino acids alone. Moreover, advantages of increased potency and protease stability are often observed. Our understanding of the biosynthesis of these D-amino acid-containing peptides is still in its infancy. Nevertheless, the discovery of a novel peptide isomerase from the venom of the Agelenopsis aperta spider provides some important clues to explain the incorporation of single D-amino acid residues within a peptide chain. Given its high homology with other serine proteases, the isomerase may represent an opportune mutation in response to evolutionary pressures. Yet, is the isomerase a unique exception or simply the first in a class of enzymes of varying substrate specificity capable of synthesizing D-amino acid-containing peptides? To be sure, much more remains to be explored about the precise timing and mechanism of the isomerization process, in addition to obtaining further structural data on the enzyme itself. Therein lies the continuation of this fascinating story in enzyme biochemistry.

Amino Acid Isomerases↗