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At least 919 records · Page 51Linked to original sources
PubMed1991

Early evolution and the origin of eukaryotes.

Our understanding of evolutionary relationships in the eukaryotic world has been revolutionized by molecular systematics. Phylogenies based upon comparisons of rRNAs define five major eukaryotic assemblages plus a series of paraphyletic protist lineages. Comparison of conserved genes that were duplicated prior to the divergence of eubacteria, archaebacteria, and eukaryotes, positions the root of the universal tree within the eubacterial line of descent. In this review a novel model is presented which uses the rRNA and protein based phylogenies to describe the evolutionary origins of eukaryotes.

Animal Population Groups↗
PubMed1973

Relatedness among contractile and membrane proteins: evidence for evolution from common ancestral genes.

A statistical method for quantifying the relatedness among proteins was used to perform 2926 paired comparisons of amino-acid composition among 77 contractile and membrane-associated proteins from diverse species and sources. Relatedness of amino-acid compositions correlates with homology of amino-acid sequence. A high degree of relatedness was detected among K(+)-dependent membrane ATPase of Streptococcus faecalis, coupling factors F(1) and CF(1) from mitochondria and chloroplasts, outer fiber protein of cilia, ciliary dynein, tubulin, various actins, and myosin subfragment S-1. Heavy meromyosin and tropomyosin were related to each other but not to the first group of proteins. Differences in the degree of methylation may account for some differences in physiological function. Because of their diverse sources, the high degree of relatedness among these proteins is more compatible with evolution from common ancestral genes than with convergent evolution. Squid axon filarin, molluscan paramyosin, and bacterial flagellins appear to be unrelated either to each other or to any of the other proteins studied. Existence of persistent homologies among so many diverse proteins implies conservation of genetic information during evolution by utilization of codons for preferred amino-acid sequences in various proteins.

Actins↗
PubMed1995

Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer.

Phylogenetic relationships, rates of evolution, and codon usage were investigated in a family of retrotransposons (SURL elements) found in echinoids. The phylogeny of SURL element reverse transcriptase sequences from 10 echinoid species clearly shows the phylogenetic signature of the host taxa as well as paralogous sequences that diverged prior to speciation events. Two subfamilies (1 and 5) of SURL element reverse transcriptase sequences are recognized that diverged prior to the radiation of the Echinometridae. Comparisons of synonymous versus nonsynonymous substitutions indicate that SURL elements have been active in echinoid genomes and have evolved under purifying selection for millions of years. Rates of synonymous substitution for reverse transcriptase are similar to rates of single-copy DNA evolution and to rates of synonymous substitution for the H3 and H4 histone genes, contradicting the assumption that rates of evolution are accelerated in retrotransposons. Finally, codon usage in SURL elements is biased for codons ending in A or U relative to 42 sea urchin nuclear genes. Biased codon usage is sometimes cited as evidence for horizontal transfer, but in the case of SURL elements this bias occurs in spite of a long history of vertical transmission rather than because of horizontal transfer.

Animals↗
PubMed1984

Papillomavirus genomes: sequences and consequences.

The complete nucleotide sequences of four papillomavirus genomes recently determined (human papillomavirus types 1a and 6b, bovine papillomavirus type 1, and the Shope cottontail rabbit papillomavirus) shed light on the molecular genetics of these epitheliotropic viruses. The organization of the four genomes is very similar, and their comparative analysis suggests new hypotheses about the nature of the viral proteins, their involvement in virus structure, and their interaction with the host cell, the terminally differentiating keratinocyte. It also allows us to consider, at the molecular level, the problem of papillomaviruses' host range and evolutionary relationship.

Amino Acid Sequence↗
PubMed1975

Relation of an evolutionary mechanism to differentiation.

It is believed that new gene products and differentiations arise during evolution by the creation of new members of families of repeated DNA sequences which undergo diversification and take on new functions, while still retaining some common sequences indicating their common ancestry. Since some of the sequences of such DNA families control differentiations that occur in present-day embryos, it appears that members of such families formed during evolution are active in development. The presence of partially homologous proteins in related types of cells, as well as the labile pattern of determination and differentiation of these cells, supports this idea. The ontogenetic sequence of differentiation follows the phylogenetic one and this may occur because the more conservative members of any family of DNA sequences are more reiterated and transcribe more copies of RNA.

Animals↗
PubMed1984

Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses.

The nucleotide sequence of the 3035 residues of RNA 2 (Mr 1.03 X 10(6) ) of the Q strain of cucumber mosaic virus (CMV) was determined by sequencing M13 clones of the RNA 2 cDNA and by dideoxy sequencing using primers prepared either from M13 clones or by chemical synthesis. A single long open reading frame starts at the second AUG from the 5' end of RNA 2 and encodes 839 amino acids (Mr 94333). This frame has flanking regions of 92 nucleotides at the 5' terminus and 423 nucleotides at the 3' terminus. Computer analysis of the nucleotide sequence showed that CMV RNA 2 has a significant homology with RNA 2 of brome mosaic virus (BMV) and alfalfa mosaic virus (AMV) and also with a region for tobacco mosaic virus (TMV) RNA encoding the read-through part of the 183-kDa protein. About 400 amino acids in the central region of the CMV RNA 2 translation product have a striking homology with the corresponding proteins encoded by BMV and AMV and with the read-through part of the TMV 183-kDa protein. Hydrophobicity plots of CMV and BMV RNA translation products also had apparent similarities. It is concluded that CMV is related to BMV, AMV and TMV in order of increasing evolutionary divergence.

Amino Acid Sequence↗
PubMed1980

Silent nucleotide substitutions and the molecular evolutionary clock.

Half of the nucleotide substitutions during the evolutionary divergence of genes in animals, bacteria, and viruses are silent changes. These result from an inherent biochemical property of DNA and are fixed by genetic drift. Evolution may be viewed as a device for protecting DNA molecules from extinction.

Animals↗
PubMed2006

An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices.

BACKGROUND: Quantitative descriptions of amino acid similarity, expressed as probabilistic models of evolutionary interchangeability, are central to many mainstream bioinformatic procedures such as sequence alignment, homology searching, and protein structural prediction. Here we present a web-based, user-friendly analysis tool that allows any researcher to quickly and easily visualize relationships between these bioinformatic metrics and to explore their relationships to underlying indices of amino acid molecular descriptors. RESULTS: We demonstrate the three fundamental types of question that our software can address by taking as a specific example the connections between 49 measures of amino acid biophysical properties (e.g., size, charge and hydrophobicity), a generalized model of amino acid substitution (as represented by the PAM74-100 matrix), and the mutational distance that separates amino acids within the standard genetic code (i.e., the number of point mutations required for interconversion during protein evolution). We show that our software allows a user to recapture the insights from several key publications on these topics in just a few minutes. CONCLUSION: Our software facilitates rapid, interactive exploration of three interconnected topics: (i) the multidimensional molecular descriptors of the twenty proteinaceous amino acids, (ii) the correlation of these biophysical measurements with observed patterns of amino acid substitution, and (iii) the causal basis for differences between any two observed patterns of amino acid substitution. This software acts as an intuitive bioinformatic exploration tool that can guide more comprehensive statistical analyses relating to a diverse array of specific research questions.

Amino Acid Sequence↗