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PubMed1982

Molecular evolution in papova viruses and in bacteriophages.

By comparing the DNA sequences of three eukaryotic papova viral genomes, we attempt to show the very close relative phylogeny among the viral species and their host species, and that therefore the viral species appear to have evolved with their hosts. A comparison of the DNA data also reveals that the rate of nucleotide substitutions at the third positions of codons is much faster than at the first and second positions, though the rate varies depending upon the genes. The estimated rates of amino acid substitutions in homologous genes among the three virus species appear to be considerably faster than the rates known for various vertebrate genes. The comparison reveals further that the rate of silent substitutions is faster than that of replacement substitutions. The DNA sequence data on bacteriophages phi X174 and G4 enable us to examine the patterns of nucleotide substitutions in overlapping genes as well as in nonoverlapping genes. It then becomes evident that overlapping genes have a quite different substitutional pattern with respect to the position of nucleotides in codons than do nonoverlapping sequences. In nonoverlapping regions the third positions usually change the fastest among the three codon positions. This pattern does not apply to overlapping genes, which are coded in the same region but with different reading frames. It will be shown that the younger of the two overlapping genes appears to be very tolerant to nucleotide substitutions at any codon position. Further more, the rate of substitution at each nucleotide site appears to be determined by the rate of the corresponding site in the older of the two overlapping genes.

BK Virus↗
PubMed1987

Proteins, exons and molecular evolution.

The discovery of the eukaryotic gene structure has prompted research into the potential relationship between protein structure and function and the corresponding exon/intron patterns. The exon shuffling hypothesis put forward by Gilbert and Blake suggests the encodement of structural and functional protein elements by exons which can recombine to create novel proteins. This provides an explanation for the relatively rapid evolution of proteins from a few primordial molecules. As the number of gene and protein structures increases, evidence of exon shuffling is becoming more apparent and examples are presented both from modern multi-domain proteins and ancient proteins. Recent work into the chemical properties and catalytic functions of RNA have led to hypotheses based upon the early existence of RNA. These theories suggest that the split gene structure originated in the primordial soup as a result of random RNA synthesis. Stable regions of RNA, or exons, were utilised as primitive enzymes. In response to selective pressures for information storage, the activity was directly transferred from the RNA enzymes or ribozymes, to proteins. These short polypeptides fused together to create larger proteins with a wide range of functions. Recent research into RNA processing and exon size, discussed in this review, provides a clearer insight into the evolutionary development of the gene and protein structure.

Biological Evolution↗
PubMed1988

Molecular evolution of the 5'-terminal domain of large-subunit rRNA from lower eukaryotes. A broad phylogeny covering photosynthetic and non-photosynthetic protists.

This paper summarizes the present status of an analysis of protist phylogeny using rapid partial sequencing of 28S rRNA. Data from 12 protistan phyla are now available and have been used to construct a tentative dendrogram based on a distance matrix method. The tree is robust and has considerable internal consistency. The following salient points are observed: a number of flagellate groups (particularly Euglenozoa) emerge very early among eukaryotes, whereas ciliates and dinoflagellates emerge late, suggesting that some characteristics that had been considered as primitive may in fact be derived. Both chlorophytic and chromophytic photosynthetic protists emerge very late in the tree, close to the Metazoa-Metaphyta-Fungi radiation, suggesting relatively late occurrence of the photosynthetic symbiosis. Taxonomic and phylogenetic information is also obtained within a phylum where rRNA of enough species are sequenced. A deep trichotomy is thus observed within the ciliates. The data are discussed with respect to classical protist phylogenies.

Animals↗
PubMed1986

Nucleotide sequence and molecular evolution of two tomato genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase.

We have isolated and sequenced two cDNA clones (LESS5 and LESS17) encoding the small subunit of ribulose-1,5-bisphosphate carboxylase of tomato (Lycopersicon esculentum). At the nucleotide level, the protein-coding regions of these genes are 85% conserved, while the untranslated 3' regions are only 55% conserved. Comparison with rbcS genes from other species of Solanaceae suggests that the tomato LESS5 gene, the Nicotiana tabacum NTSS23 gene and the Petunia hybrida SSU8 gene are orthologous members of the rbcS gene family. In addition, the tomato gene LESS17, and the Petunia hybrida gene SSU611, may also be orthologous, since their untranslated 3' regions are related. There is a large difference between the two tomato rbcS genes in the frequency of the CG dinucleotide. This difference may reflect different levels of methylation, and therefore expression, of the tomato genes. Many of the differences involving the CG dinucleotide can be represented as transitions between C and T on the noncoding strand. Such changes are consistent with observations that methylated cytosines are hot-spots for transitions.

Base Sequence↗
PubMed1993

Fractal landscapes and molecular evolution: modeling the myosin heavy chain gene family.

Mapping nucleotide sequences onto a "DNA walk" produces a novel representation of DNA that can then be studied quantitatively using techniques derived from fractal landscape analysis. We used this method to analyze 11 complete genomic and cDNA myosin heavy chain (MHC) sequences belonging to 8 different species. Our analysis suggests an increase in fractal complexity for MHC genes with evolution with vertebrate > invertebrate > yeast. The increase in complexity is measured by the presence of long-range power-law correlations, which are quantified by the scaling exponent alpha. We develop a simple iterative model, based on known properties of polymeric sequences, that generates long-range nucleotide correlations from an initially noncorrelated coding region. This new model-as well as the DNA walk analysis-both support the intron-late theory of gene evolution.

Actins↗
PubMed1989

The genetic code as a clue to understanding of molecular evolution.

The genetic code is comprised of a system concerning the distribution of doublets of the first two codon bases among amino acids. According to this system a definite order in the relative distribution of the first and the second codon bases coincides with a definite order among the common amino acids and their distribution for the number of hydrogen atoms per molecule (an unexpected parameter). The pattern of the relative distribution of the first and the second codon bases suggests it originated from a crystalline-like structure in which the set of bases AUGC served as an elementary structural unit and the base doublets played the role of structural analogs to the amino acids. These hypothetical crystalline-like aggregates are composed of the free molecules of amino acids and bases, and although different in their composition, should have an even number of hydrogen atoms per standard structural module.

Amino Acids↗
PubMed2000

Molecular evolution of flower development.

Flowers, as reproductive structures of the most successful group of land plants, have been a central focus of study for both evolutionists and ecologists. Recent advances in unravelling the genetics of flower development have provided insight into the evolution of floral structures among angiosperms. The study of the evolution of genes that control floral morphogenesis permits us to draw inferences on the diversification of developmental systems, the origin of floral organs and the selective forces that drive evolutionary change among these plant reproductive structures.

Journal Article↗