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Results for “synonymous codons”

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At least 127 records · Page 7Linked to original sources

PubMed1988

cDNA cloning and sequence determination of pig gastric (H+ + K+)-ATPase.

Complementary DNA to pig gastric mRNA encoding (H+ + K+)-ATPase was cloned, and its amino acid sequence was deduced from the nucleotide sequence. The enzyme contained 1034 amino acid residues (Mr. 114,285) including the initiation methionine. The sequence of pig (H+ + K+)-ATPase was highly homologous with that of the corresponding enzyme from rat, but had high degree of synonymous codon changes. Potential sites of phosphorylation by cAMP-dependent protein kinase and N-linked glycosylation sites were identified. The amino terminal region contained a lysine-rich sequence similar to that of the alpha subunit of (Na+ + K+)-ATPase, although a cluster of glycine residues was inserted into the sequence of the (H+ + K+)-ATPase. As the pig enzyme is advantageous for biochemical studies, the information of the primary structure is useful for further detailed studies.

Adenosine Triphosphatases↗

PubMed1983

DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins.

The complete DNA sequences of two loci encoding H3 and H4 histones in Saccharomyces cerevisiae have been determined. Each locus contains one H3 and one H4 gene. The genes at each locus are divergently transcribed and the coding sequences are separated by 646 base-pairs at one locus and 676 base-pairs at the other. The H3 genes code for identical histone H3 proteins and the H4 genes code for identical histone H4 proteins. The yeast proteins differ from histones H3 and H4 of calf by 15 and 8 amino acid substitutions, respectively, and these differences are largely confined to the carboxy-terminal halves of the proteins. The genes demonstrate a bias in synonymous codon usage similar to that noted for other yeast genes. This bias is confined to the coding sequences of the genes and is specific for the reading frame encoding the proteins. The coding sequence of each gene is flanked on both sides by DNA with an A + T content of 70 to 80%. Possible regulatory sequences are located relative to the 5' and 3'-termini of the histone H3 and H4 RNA transcripts.

Base Sequence↗

PubMed1991

Prime numbers and the amino acid code: analogy in coding properties.

Natural numbers are characterized as being odd or even, prime or non-prime. If the quaternary information units of (DNA or RNA) nucleotide bases are assigned as 0 (for A), 1 (C), 2 (U or T) and 3 (G), then a unique set of amino acid numbers can be obtained by comparing the properties of numbers and coding properties. These numbers are: 0 for "stop" signals, 1 for Trp, 2 for Ile and 3 for Met. For other codons, synonymous quartets follow exclusively the P1 number series (prime numbers of the form 4n + 1); doublets mostly follow the P3 series (primes with quaternary remainder 3). A "one-to-one correspondence" between these numbers and the genetic code is established by considering their combinatorial specificities.

Amino Acid Sequence↗

PubMed1973

Nucleotide sequence divergence in the -chain-structural genes of tryptophan synthetase from Escherichia coli, Salmonella typhimurium, and Aerobacter aerogenes.

Two different estimates were obtained for the extent of nucleotide sequence divergence in the structural genes of the tryptophan synthetase alpha-chains of Escherichia coli, Salmonella typhimurium, and Aerobacter aerogenes. One estimate was based on comparisons of the amino acid sequences of the respective alpha chains. The other was derived from measurements of the thermal stability of RNA-DNA hybrids formed with phage DNA carrying the alpha-chain structural gene of E. coli and labeled messenger RNA from the three bacterial species. Comparison of the two estimates suggests that during the course of evolution synonymous codon changes have accumulated in the alpha-chain-structural genes.

Amino Acid Sequence↗

PubMed1977

Molecular evolution of human and rabbit beta-globin mRNAs.

The primary structures of human and rabbit beta-globin mRNAs are compared. Using as a standard the extent of nucleotide substitutions inferred from the hypervariable amino acid residues of fibrinopeptides A and B, which are thought to change largely by neutral evolution, we show that not all silent mutations in globin mRNA are neutral. The divergence of the sequences is limited in part by the selective usage of synonymous codons. The divergent nucleotides tend to be distributed nonrandomly: in the coding region silent substitutions are most rare in segments that are also deficient in substitutions leading to replacements.

Animals↗

PubMed1966

Problems in protein biosynthesis.

Outline of the steps in protein synthesis. Nature of the genetic code. The use of synthetic oligo- and polynucleotides in deciphering the code. Structure of the code: relatedness of synonym codons. The wobble hypothesis. Chain initiation and N-formyl-methionine. Chain termination and nonsense codons. Mistakes in translation: ambiguity in vitro. Suppressor mutations resulting in ambiguity. Limitations in the universality of the code. Attempts to determine the particular codons used by a species. Mechanisms of suppression, caused by (a) abnormal aminoacyl-tRNA, (b) ribosomal malfunction. Effect of streptomycin. The problem of "reading" a nucleic acid template. Different ribosomal mutants and DNA polymerase mutants might cause different mistakes. The possibility of involvement of allosteric proteins in template reading.

Genetic Code↗

PubMed1991

Transient mutators: a semiquantitative analysis of the influence of translation and transcription errors on mutation rates.

A population of bacteria growing in a nonlimiting medium includes mutator bacteria and transient mutators defined as wild-type bacteria which, due to occasional transcription or translation errors, display a mutator phenotype. A semiquantitative theoretical analysis of the steady-state composition of an Escherichia coli population suggests that true strong genotypic mutators produce about 3 x 10(-3) of the single mutations arising in the population, while transient mutators produce at least 10% of the single mutations and more than 95% of the simultaneous double mutations. Numbers of mismatch repair proteins inherited by the offspring, proportions of lethal mutations and mortality rates are among the main parameters that influence the steady-state composition of the population. These results have implications for the experimental manipulation of mutation rates and the evolutionary fixation of frequent but nearly neutral mutations (e.g., synonymous codon substitutions).

Bacteria↗

PubMed1983

The nucleotide sequence of myosin light chain (L-2A) mRNA from embryonic chicken cardiac muscle tissue.

The nucleotide sequence of a cDNA clone (pML10) for chicken cardiac myosin light chain is described. The cDNA insert contains 613 nucleotides representing the entire coding sequence, with the exception of nine NH2-terminal amino acids, and the full 3'-non-coding region of 146 nucleotides. The missing 5' terminus of the mRNA, not represented in the clone pML10, was obtained by extension of the cDNA using a 43 nucleotide long internal EcoR1 fragment as a primer. The non-coding region contains several direct and inverted repeated sequences and the polyadenylation signal sequence AATAAA. The coding portion exhibits non-random usage of synonymous codons with a strong bias for codons ending in G and C.

Amino Acid Sequence↗

PubMed1985

The secondary structure of mRNAs from Escherichia coli: its possible role in increasing the accuracy of translation.

A secondary structure model was proposed for mRNAs during translation (in a polysome) where the secondary structure is described by a set of small unbranched hairpins. Computer simulation experiments reveal that the number of hairpins is much greater (P less than 10(-6) in highly expressed mRNAs from E. coli as compared with the random sequences coding for the same amino acid sequence, i.e. certain synonymous codons are used in definite mRNA positions to increase the number of hairpins. No constraints on the amino acid sequence, which would affect the secondary structure of mRNAs, were found. The codons UGU, UGC (Cys), GCC (Ala), ACA, ACG (Thr), CCU, CCC (Pro), etc. translated by minor tRNAs were found to occur significantly more frequently in the position 5' to the hairpins than the other codons translated by major tRNAs (P less than 5.10(-6). This correlation leads to the hypothesis that the process of hairpin unfolding can increase the time of translocation from the A to P ribosome site of the codon 5' to the hairpin, thus decreasing the probability of translational error (the latter would likely occur more frequently in the codons translated by minor tRNAs).

Base Sequence↗

PubMed1991

Levels of tRNAs in bacterial cells as affected by amino acid usage in proteins.

Transfer RNAs of Mycoplasma capricolum were separated by two-dimensional polyacrylamide gel electrophoresis, and the relative abundance of each of the 28 known tRNA species was measured. There existed a correlation between the relative amount of isoacceptor tRNAs and the frequency in choosing synonymous codons that could be translated by the isoacceptors. Furthermore, it was observed that the total amount of tRNAs for a particular amino acid was paralleled by the composition of the amino acid in ribosomal proteins. A similar relationship was obtained from reexamination of the previous data on Escherichia coli tRNAs, suggesting that the amount of tRNAs for an amino acid is affected by the usage of the amino acid in proteins.

Amino Acid Sequence↗

PubMed1979

Secondary structure of MS2 phage RNA and bias in code word usage.

Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and/or G. This nature is interpreted as a result of selective constraint which stabilises the secondary structure of the single-stranded RNA genome of the MS2 phage.

Base Sequence↗

PubMed1985

Sequence of the ebgA gene of Escherichia coli: comparison with the lacZ gene.

We have sequenced the ebgA (evolved beta-galactosidase) gene of Escherichia coli K12. The sequence shows 50% nucleotide identity with the E. coli lacZ gene, demonstrating that the two genes are related by descent from a common ancestral gene. Comparison of the two sequences suggests that the ebgA gene has recently been under selection. A significant excess of identical, rather than synonymous, codons used to encode identical amino acids at the same positions in the aligned sequences implies that some form of selection is operating directly at the DNA level. This selection is independent of, and in addition to, selection based on codon usage or on function of the gene products.

Amino Acid Sequence↗

PubMed1986

DNA and the neutral theory.

The neutral theory claims that the great majority of evolutionary changes at the molecular (DNA) level are caused not by Darwinian selection but by random fixation of selectively neutral or nearly neutral mutants. The theory also asserts that the majority of protein and DNA polymorphisms are selectively neutral and that they are maintained in the species by mutational input balanced by random extinction. In conjunction with diffusion models (the stochastic theory) of gene frequencies in finite populations, it treats these phenomena in quantitative terms based on actual observations. Although the theory has been strongly criticized by the 'selectionists', supporting evidence has accumulated over the years. Particularly, the recent outburst of DNA sequence data lends strong support to the theory both with respect to evolutionary base substitutions and DNA polymorphism, including rapid evolutionary base substitutions in pseudogenes. In addition, the observed pattern of synonymous codon choice can now be readily explained in the framework of this theory. I review these recent findings in the light of the neutral theory.

Animals↗

PubMed1983

Sequence analysis of the cloned mRNA coding for glyceraldehyde-3-phosphate dehydrogenase from chicken heart muscle.

Using a cloned cDNA (pGAP30) the nucleotide sequence for chicken glyceraldehyde-3-phosphate dehydrogenase mRNA has been determined. The cDNA insert contains 1051 nucleotides representing the amino acid coding sequence, with the exception of 49 NH2-terminal amino acids, and includes the entire 3'-noncoding region. Sequence information on the missing 5' terminus of the mRNA, not represented in the clone pGAP30, was obtained by extension of the cDNA using an 85-nucleotide-long internal fragment as a primer. Thus the sequence of 310 amino acids of chicken glyceraldehyde-3-phosphate dehydrogenase representing 93% of the complete primary structure could be derived. The coding portion exhibits non-random utilization of synonymous codons with a strong bias for codons with G or C at the third position. The non-coding region contains several octanucleotides which are repeated and shows a potentially stable stem-and-loop structure located towards the end of the mRNA. Hypothetical functional implications of the putative secondary structure are discussed.

Amino Acid Sequence↗

PubMed1987

Massive overproduction of dihydrofolate reductase in bacteria as a response to the use of trimethoprim.

Among several observations of greatly increased levels of chromosomal dihydrofolate reductase as a cause of resistance to high concentrations of the antifolate drug trimethoprim, in clinically isolated bacteria, one is described here of a strain of Escherichia coli overproducing dihydrofolate reductase several hundredfold. The chromosomally located resistance gene of this strain was isolated, inserted into a plasmid vector, and analyzed for its nucleotide sequence. The structural gene for the overproduced dihydrofolate reductase was found to be identical to that of E. coli K12, with nine exceptions, of which seven resulted in synonymous codon usage. Two transversions resulted in a substitution of Gly or Trp at amino acid position 30, and of Gln for Glu at position 154. Six of the nine base changes resulted in codons more frequently used. The Gly substitution which leads to a less commonly used codon, was thought to relate to the observed threefold increase in Ki for trimethoprim. Furthermore, a C----T transition was found in the -35 region of the promoter, increasing its homology with the E. coli consensus promoter sequence. In the ribosome-binding area of the resistant strain, finally, seven base changes were observed, two of which resulted in a five-base sequence of complementarity with the 3'-end of ribosomal 16S RNA. The distance between the -10 site of the promoter and the start codon for translation was finally increased one base pair by the insertion of an A at position +9 in the resistant strain. These genetic changes towards more efficient transcriptional and translational start sequences and towards increased mRNA expressivity are interpreted to reflect an evolutionary adaptation to the presence of antifolates.

Base Sequence↗

PubMed1989

Chromosomal location and evolutionary rate variation in enterobacterial genes.

The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.

Bias↗

PubMed1990

Complementarity of Bacillus subtilis 16S rRNA with sites of antibiotic-dependent ribosome stalling in cat and erm leaders.

Inducible cat and erm genes are regulated by translational attenuation. In this regulatory model, gene activation results from chloramphenicol- or erythromycin-dependent stalling of a ribosome at a precise site in the leader region of cat or erm transcripts. The stalled ribosome is believed to destabilize a downstream region of RNA secondary structure that sequesters the ribosome-binding site for the cat or erm coding sequence. Here we show that the ribosome stall sites in cat and erm leader mRNAs, designated crb and erb, respectively, are largely complementary to an internal sequence in 16S rRNA of Bacillus subtilis. A tetracycline resistance gene that is likely regulated by translational attenuation also contains a sequence in its leader mRNA, trb, which is complementary to a sequence in 16S rRNA that overlaps with the crb and erb complements. An in vivo assay is described which is designed to test whether 16S rRNA of a translating ribosome can interact with the crb sequence in mRNA in an inducer-dependent reaction. The assay compares the growth rate of cells expressing crb-86 with the growth rate of cells lacking crb-86 in the presence of subinhibitory levels of inducers of cat-86, chloramphenicol, fluorothiamphenicol, amicetin, or erythromycin. Under these conditions, crb-86 retarded growth. Deletion of the crb-86 sequence, insertion of ochre mutations into crb-86, or synonymous codon changes in crb-86 that decreased its complementarity with 16S rRNA all eliminated from detection inducer-dependent growth retardation. Lincomycin, a ribosomally targeted antibiotic that is not an inducer of cat-86, failed to selectively retard the growth of cells expressing crb-86. We suggest that cat-86 inducers enable the crb-86 sequence in mRNA to base pair with 16S rRNA of translating ribosome. When the base pairing is extensive, as with crb-86, ribosomes become transiently trapped on crb and are temporarily withdrawn from protein synthesis to the extent that growth rate declines. Site-specific positioning of an antibiotic-stalled ribosome is a hallmark of the translational attenuation model. The proposed rRNA-mRNA interaction may precisely position the ribosome on the stall site and perhaps contributes to stabilizing the ribosome leader mRNA complex.

Bacillus subtilis↗

PubMed2026

Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).

The genus Abutilon Mill. (Malvaceae) comprises approximately 178 species distributed across tropical and subtropical regions, many of which hold significant ornamental, economic, and medicinal value; yet its taxonomic classification remains challenging. In this study, six species were sequenced from herbarium specimens, and the chloroplast (cp.) genomes of ten additional species were assembled de novo from publicly available raw data. Three previously reported cp. genomes were also incorporated to characterise cp. genome structure, identify polymorphic loci, and perform phylogenetic analyses. The cp. genomes ranged from 159,458 to 160,454 bp and exhibited the typical quadripartite structure, with each genome containing 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA) that showed conserved content and organisation. These genomes exhibited high similarity in GC content, inverted repeat boundaries, relative synonymous codon usage, amino acid frequencies, and substitution patterns. However, notable variation was observed in the total number of simple sequence repeats, ranging from 70 to 97 per genome. Selection analyses indicated predominant purifying selection, with evidence of episodic positive selection detected in rpoC2, rbcL, and ycf1. Two codons in rbcL were clade-specific and provided phylogenetic signal distinguishing Australian and Old World pantropical species. Nucleotide diversity analysis identified six highly polymorphic intergenic spacers (trnH-psbA, rps19-rpl2, psbT-pbf1, psaC-ndhD, trnR-atpA, and ndhJ-ndhK) that may be suitable for taxonomic studies. The phylogeny from maximum likelihood (ML) and Bayesian inference (BI) resolved two major clades: one comprising an exclusively Australian lineage occurring predominantly in arid and semi-arid environments, and the other a pantropical lineage spanning multiple continents. Abutilon grandifolium was recovered as sister to the remaining sampled Abutilon taxa in both ML and BI analyses, although no biogeographic origin inference can be drawn from this placement pending broader taxon sampling and integration of nuclear genomic data. These findings provide insights into the evolutionary dynamics of the cp. genome in Abutilon and offer a foundational genomic framework for refining Abutilon taxonomy.

Genome, Chloroplast↗