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Results for “Genetic code evolution”

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At least 865 records · Page 48Linked to original sources
PubMed1981

The evolution of alpha-fetoprotein and albumin. I. A comparison of the primary amino acid sequences of mammalian alpha-fetoprotein and albumin.

The amino acid sequence of mouse alpha-fetoprotein has been deduced from the nucleotide sequence of its mRNA and three chimeric plasmids containing overlapping segments of its cDNA. A comparison of the amino acid sequence with that of either human and bovine albumin reveals in each case a 32% conservation of primary sequence. In addition, using the regularly spaced positions of cystine bridges, a 2-dimensional structure was generated, which revealed the presence of 3 closely related domains within alpha-fetoprotein. The structures of these domains are identical with the triplicated domains previously observed in several mammalian albumins. These homologies lend strong circumstantial evidence to the proposal that these two proteins arose in evolution as the consequence of a duplication in a common tripartite ancestral gene.

Albumins↗
PubMed1997

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

Animals↗
PubMed1982

Evolution of a complex eukaryotic gene.

Our current efforts to understand the evolutionary origin of the ovomucoid gene are reviewed. Sequence analyses have suggested that introns were present in the primordial ovomucoid gene before birds and mammals diverged, about 300 million years ago. Our work suggests that the present ovomucoid gene has evolved from primordial ovomucoid gene by two separate intragenic duplications followed by the addition of a final segment which codes for a secretory signal sequence. The 3 domains of the secreted peptide and also the signal sequence are constructed by an apparent assembly of exons which code for individual peptide segments. The exact position of introns within the ovomucoid gene has been defined and the results support the theory that introns separate gene segments that code for functional domains of proteins and provide insight into the manner by which eukaryotic genes were constructed during the process of evolution.

Animals↗
PubMed2005

Fishing for the secrets of vertebrate evolution in threespine sticklebacks.

The threespine stickleback (Gasterosteus aculeatus) is rapidly emerging as a new model genetic system to study questions at the interface of evolution and development. The relatively rapid and recent diversification of this small teleost fish, combined with the development of genetic and genomic tools for this fish, provides an unprecedented opportunity to identify the genetic and molecular basis of morphological variation in natural populations of vertebrates. Recently, the genes underlying two different adaptive morphological traits in stickleback have been identified. This work has provided answers to four longstanding questions in the field of evolution and development: (1) How many genes underlie morphological variation in natural populations? (2) What are the genes that underlie morphological variation in natural populations? (3) Do coding or regulatory mutations underlie morphological evolution? (4) What is the molecular and genetic basis of parallel morphological evolution? Because stickleback populations also display natural variation in morphology, life history, physiology, and behavior, extending the approaches used to identify the genetic basis of morphological variation in sticklebacks to other phenotypes is sure to yield further important insights into the genetic and developmental basis of diversity in natural populations.

Adaptation, Biological↗
PubMed1987

Transitions, transversions, and the molecular evolutionary clock.

Nucleotide substitutions in the form of transitions (purine-purine or pyrimidine-pyrimidine interchanges) and transversions (purine-pyrimidine interchanges) occur during evolution and may be compiled by aligning the sequences of homologous genes. Referring to the genetic code tables, silent transitions take place in third positions of codons in family boxes and two-codon sets. Silent transversions in third positions occur only in family boxes, except for A = C transversions between AGR and CGR arginine codons (R = A or G). Comparisons of several protein genes have been made, and various subclasses of transitional and transversional nucleotide substitutions have been compiled. Considerable variations occur among the relative proportions of transitions and transversions. Such variations could possibly be caused by mutator genes, favoring either transitions or, conversely, transversions, during DNA replication. At earlier stages of evolutionary divergence, transitions are usually more frequent, but there are exceptions. No indication was found that transversions usually originate from multiple substitutions in transitions.

Animals↗
PubMed1995

Differential codon usage for conserved amino acids: evidence that the serine codons TCN were primordial.

The availability of specialized sequence databanks for Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis made it possible to build a set of 105 protein-coding genes that are homologous in these three species. An analysis of the triplets at both the nucleotide and amino acid level revealed that the codon bias of some amino acids are significantly higher at conserved rather than at non-conserved positions. Comparisons of homologous genes in E. coli and Salmonella typhimurium, and in S. cerevisiae and Drosophila melanogaster, led to the same conclusion. A special case was made for serine in E. coli, whose major codon is AGC for non-conserved and TCC for conserved residues. We interpret this observation as evidence that the primordial codons for serine were TCN, while codons AGY appeared later. This conclusion is substantiated by an analysis of the codon usage of catalytic serine residues in ancient, ubiquitous and essential proteins (ATP synthases and topoisomerases). It is shown that in these proteins the proportion of the catalytic serine residues coded by TCN is significantly higher than the one expected from the overall codon usage of serine residues.

Amino Acid Sequence↗
PubMed2004

Evolving new genetic codes.

Although the genetic code is almost universal, natural variations exist that have caused evolutionary biologists to speculate about codon evolution. There are two predominant hypotheses that specify either a gradual (ambiguous intermediate) or stochastic (codon capture) change in the code. These hypotheses are similar to two biotechnology techniques that have been used to engineer the genetic code: a 'top down' approach, in which the whole organism is evolved for the ability to incorporate unnatural amino acids, and a 'bottom up' approach, in which aminoacyl-tRNA synthetases and their cognate tRNAs are engineered. The biotechnology experiments provide insights into natural codon evolution, and a combination of these approaches should enable the evolution of organisms that can incorporate unnatural amino acids throughout their proteomes.

Journal Article↗
PubMed1983

Homology between coding and noncoding sequences within the human class I HLA antigen gene.

In our previous paper, we identified 32 recurring base oligomers (1 decamer, 4 octamers, 9 heptamers and 18 hexamers) within the coding sequence for the mouse class I major histocompatibility (MHC) antigen H-2Kb. The compilation of these recurring base oligomers led to the conclusion that the entire ancestral coding sequence for class 1 MHC antigens evolved from tandem repeats of the one 45 base-long primordial building block base sequence. As with most other mammalian genes, the gene for each class I MHC antigen is an admixture of coding and noncoding segments interspersed with each other. Thus, the status of noncoding segments should be clarified in relation to the concept of the primordial building block. The published 4,122 base-long sequence of human pHLA 12.4 germline gene afforded me an opportunity for clarification. Since the number of recurring base oligomers residing within the entire 4,000 + base-long sequence proved unmanageably numerous, the two portions 1,200 bases in the total length were singled out. Within these portions containing five noncoding and four coding segments, noncoding and coding segments shared 1 nonomer, 3 octamers, 6 heptamers and 5 hexamers; all the above-noted base oligomers were derived from different parts of the same 45 base-long primordial building block. It was thus concluded that not only the coding segments, but the entire ancestral gene for class I MHC antigens evolved from tandem repeats of the 45-base-long primordial building block. This new concept of primordial building block was discussed in relation to the mechanism of evolution by gene duplication.

Base Sequence↗
PubMed1990

Genetic code 1990. Outlook.

The genetic code is evolving as shown by 9 departures from the universal code: 6 of them are in mitochondria and 3 are in nuclear codes. We propose that these changes are preceded by disappearance of a codon from coding sequences in mRNA of an organism or organelle. The function of the codon that disappears is taken by other, synonymous codons, so that there is no change in amino acid sequences of proteins. The deleted codon then reappears with a new function. Wobble pairing between anticodons and codons has evolved, starting with a single UNN anticodon pairing with 4 codons. Directional mutation pressure affects codon usage and may produce codon reassignments, especially of stop codons. Selenocysteine is coded by UGA, which is also a stop codon, and this anomaly is discussed. The outlook for discovery of more changes in the code is favorable, and open reading frames should be compared with actual sequential analyses of protein molecules in this search.

Anaerobiosis↗
PubMed2006

Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.).

While evolution of coding sequences has been intensively studied, diversification of noncoding regulatory regions remains poorly understood. In this study, we investigated the molecular evolution of an enhancer region located 5 kb upstream of the transcription start site of the maize pericarp color1 (p1) gene. The p1 gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in maize floral organs. Distinct p1 alleles exhibit organ-specific expression patterns on kernel pericarp and cob glumes. A cob glume-specific regulatory region has been identified in the distal enhancer. Further characterization of 6 single-copy p1 alleles, including P1-rr (red pericarp/red cob) and P1-rw (red pericarp and white cob), reveals 3 distinct enhancer types. Sequence variations in the enhancer are correlated with the p1 gene expression patterns in cob glume. Structural comparisons and phylogenetic analyses suggest that evolution of the enhancer region is likely driven by gene conversion between long direct noncoding repeats (approximately 6 kb in length). Given that tandem and segmental duplications are common in both animal and plant genomes, our studies suggest that recombination between noncoding duplicated sequences could play an important role in creating genetic and phenotypic variations.

Alleles↗