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Structural studies show that fish and mammalian metallothioneins are endowed of distinctive features. In particular, the ninth cysteine residue present in the α domain of fish metallothionein is shifted of two positions with respect to the mammalian metallothionein, introducing a conformational modification in the protein structure. In addition, the fish metallothionein is less hydrophobic and more...
Our understanding of the evolutionary process would benefit from a better understanding of protein structural changes during evolution. I report that combining phylogenetic and structural analyses of the mitochondrial protein sequences allow to identify important differences between protostomes and deuterostomes mitochondrial proteins: (1) ND5, and with less intensity, ND1, ND2 and ND4, have significantly...
The H-strand of vertebrate mitochondrial DNA is left single-stranded for hours during the slow DNA replication. This facilitates C→U mutations on the H-strand (and consequently G→A mutations on the L-strand) via spontaneous deamination which occurs much more frequently on single-stranded than on double-stranded DNA. For the 12 coding sequences (CDS) collinear with the L-strand, NNY synonymous codon...
The Structurally Constrained Protein Evolution (SCPE) model simulates protein evolution by introducing random mutations into the evolving sequences and selecting them against too much structural perturbation. Given a single protein structure, the SCPE model can be used to obtain a whole set of site-dependent amino acid substitution matrices. The set of SCPE substitution matrices for a given protein...
Phylogenetic analysis of carotenoid biosynthetic pathway genes and their evolutionary rate variations were studied among eubacterial taxa. The gene sequences for the enzymes involved in this pathway were obtained for major phylogenetic groups of eubacteria (green sulfur bacteria, green nonsulphur bacteria, Gram-positive bacteria, proteobacteria, flavobacteria, cyanobacteria) and archeabacteria. These...
We study the interrelations between tRNA gene copy numbers, gene expression levels and measures of codon bias in the human genome. First, we show that isoaccepting tRNA gene copy numbers correlate positively with expression-weighted frequencies of amino acids and codons. Using expression data of more than 14,000 human genes, we show a weak positive correlation between gene expression level and frequency...
Fluctuations and increments of both C 3 and G 3 levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC 3 levels, the second shows considerable increments of the GC 3 levels in the human genes. In both data sets, the fluctuations of C 3 and G ...
Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length...
The last 50 years of molecular genetics have produced an abundance of new discoveries and data that make it useful to revisit some basic concepts and assumptions in our thinking about genomes and evolution. Chief among these observations are the complex modularity of genome organization, the biological ubiquity of mobile and repetitive DNA sequences, and the fundamental importance of DNA rearrangements...
Only 5–6% of mammalian genomes are genes; the remainders are made up primarily of transposable elements and different types of simple sequence repeat (SSRs) (micro- and minisatellites and cryptic repeats), which tend to accumulate in organisms with larger genomes. SSRs are also found at the level of protein sequences and may or may not be encoded by SSRs at the DNA sequence level. Studies of proteins...
Recent large-scale studies of evolutionary changes in gene expression among mammalian species have led to the proposal that gene expression divergence may be neutral with respect to organismic fitness. Here, we employ a comparative analysis of mammalian gene sequence divergence and gene expression divergence to test the hypothesis that the evolution of gene expression is predominantly neutral. Two...
A family of functional neogenes called Mart, related to the gag gene of Sushi-like long terminal repeat retrotransposons from fish and amphibians, is present in the genome of human (11 genes) and other primates, as well as in mouse (11 genes), rat, dog (12 genes), cat, and cow. Mart genes have lost their capacity of retrotransposition through non-functionalizing rearrangements having principally affected...
We study short-range correlations in DNA sequences with methods from information theory and statistics. We find a persisting degree of identity between the correlation patterns of different chromosomes of a species. Except for the case of human and chimpanzee inter-species differences in this correlation pattern allow robust species distinction: in a clustering tree based upon the correlation curves...
To understand the process of bilaterian evolution, we estimated ancestral gene sets at the split of plant–animal–fungi and the divergence of bilaterian animals and from 1,236,790 non-redundant genes. We, then, examined how the numbers of the gene clusters have changed since the split. As a result, we estimated the numbers of gene clusters in the ancestral gene sets of plant–animal–fungi and bilaterian...
RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural...
A two-hybrid screen with the translation initiation factor, eIF(iso)4E from Arabidopsis, identified a clone encoding a lipoxygenase type 2 [Freire, M.A., et al., 2000. Plant lipoxygenase 2 is a translation initiation factor-4E-binding protein. Plant Molecular Biology 44, 129–140], and three cDNA clones encoding the homologue of the mammalian BTF3 factor, the β subunit of the nascent polypeptide-associated...
A subtractive hybridization approach was used to identify genes that are expressed at the beginning of gastrulation. We used tester DNA complimentary to RNA (cDNA) prepared from stages 6–7 embryos (gastrula) and excess driver cDNA from stages 2–4 embryos (syncytial blastoderm) to generate a gastrula-subtracted cDNA library. A reverse Northern blot procedure used to analyze 105 subtracted clones showed...
We identified eight genes of putative RGS proteins in skin of Medaka fish using PCR amplification with degenerate primers for the RGS domain of known RGS proteins. Then, we cloned a full-length cDNA for a new RGS protein. This RGS protein was similar to human RGS3 within the RGS domain, but other parts were unique among known RGS proteins. RT-PCR analysis demonstrated that this Medaka RGS3-like protein...
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