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PubMed1992

Intron evolution: a statistical comparison of two models.

The two most frequently occurring explanations for the existence and distribution of introns in the genes of different species are: (1) introns are remnants of the original genetic material. (2) Introns were introduced during evolution. We construct mathematical models corresponding to these two explanations, and calculate the probabilities that the intron distribution in genes from different species coding for actin, alpha-tubulin, triosephosphate isomerase and superoxide dismutase are described by these models. In both models, the branch lengths as well as the structure of the corresponding evolutionary tree is taken into account. Every branch in the evolutionary tree is assumed to have its own individual rate of loss of introns for the first model and rate of gain of introns for the second model. These rate constants are estimated from the actual number of introns. Using the rate constants we stimulate the intron evolution and calculate the probabilities that the actual intron arrangements are produced. The results for actin and alpha-tubulin, which are the two genes we have the most data for, favor the model corresponding conjecture (1), i.e. the idea that introns are old. This contradicts the results from an earlier attempt to model intron evolution where almost the same data was used (Dibb & Newman, 1989, EMBO J. 8, 2015-2021).

Actins↗
PubMed1999

Directed molecular evolution.

We propose the existence of a relationship of stereochemical complementarity between gene sequences that code for interacting components: nucleic acid-nucleic acid, protein-protein and protein-nucleic acid. Such a relationship would impose evolutionary constraints on the DNA sequences themselves, thus retaining these sequences and governing the direction of the evolutionary process. Therefore, we propose that prebiotic, template-directed autocatalytic synthesis of mutally cognate peptides and polynucleotides resulted in their amplification and evolutionary conservation in contemporary prokaryotic and eukaryotic organisms as a genetic regulatory apparatus. If this proposal is correct, then the relationships between the sequences in DNA coding for these interactions constitute a life code of which the genetic code is only one aspect of the many related interactions encoded in DNA.

Base Sequence↗
PubMed2006

[Epigenetics of specific chromosome regions].

Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules that exclusively control coding and realization of genetic information. Striking plasticity of the primary structure of centromeric and telomeric DNA suggests a variety of molecular mechanisms underlying fundamental and universal functions of these key chromosome regions. The present review is an attempt to consider the current concepts on the structure of the DNA and protein components, as well as the structure of the chromatin of specific chromosome regions in eukaryotes, and the concerted evolution of these components, leading to the formation of a hierarchy of coordinated DNA-protein complexes.

Animals↗
PubMed1983

Evidence that the multifunctional polypeptides of vertebrate and fungal fatty acid synthases have arisen by independent gene fusion events.

The enoyl reductase (NADPH binding site) of rabbit mammary fatty acid synthase has been radioactively labelled using pyridoxal phosphate and sodium [3H]borohydride. Using this method we have been able to add this site to the four sites whose location has already been mapped within the multifunctional polypeptide chain of the protein. The results show that the enoyl reductase lies between the 3-oxoacylsynthase and the acyl carrier. This confirms that the active sites occur in a different order on the single multifunctional polypeptide of vertebrate fatty acid synthase and the two multifunctional polypeptides of fungal fatty acid synthase, and suggests that these two systems have arisen by independent gene fusion events.

Animals↗
PubMed2006

Meiotic recombination hotspots in plants.

Many studies have demonstrated that the distribution of meiotic crossover events along chromosomes is non-random in plants and other species with sexual reproduction. Large differences in recombination frequencies appear at several scales. On a large scale, regions of high and low rates of crossover have been found to alternate along the chromosomes in all plant species studied. High crossover rates have been reported to be correlated with several chromosome features (e.g. gene density and distance to the centromeres). However, most of these correlations cannot be extended to all plant species. Only a few plant species have been studied on a finer scale. Hotspots of meiotic recombination (i.e. DNA fragments of a few kilobases in length with a higher rate of recombination than the surrounding DNA) have been identified in maize and rice. Most of these hotspots are intragenic. In Arabidopsis thaliana, we have identified several DNA fragments (less than 5 kb in size) with genetic recombination rates at least 5 times higher than the whole-chromosome average [4.6 cM (centimorgan)/Mb], which are therefore probable hotspots for meiotic recombination. Most crossover breakpoints lie in intergenic or non-coding regions. Major efforts should be devoted to characterizing meiotic recombination at the molecular level, which should help to clarify the role of this process in genome evolution.

Animals↗
PubMedDate not supplied

Selection, recombination and history in a parasitic flatworm (Echinococcus) inferred from nucleotide sequences.

Three species of flatworms from the genus Echinococcus (E. granulosus, E. multilocularis and E. vogeli) and four strains of E. granulosus (cattle, horse, pig and sheep strains) were analysed by the PCR-SSCP method followed by sequencing, using as targets two non-coding and two coding (one nuclear and one mitochondrial) genomic regions. The sequencing data was used to evaluate hypothesis about the parasite breeding system and the causes of genetic diversification. The calculated recombination parameters suggested that cross-fertilisation was rare in the history of the group. However, the relative rates of substitution in the coding sequences showed that positive selection (instead of purifying selection) drove the evolution of an elastase and neutrophil chemotaxis inhibitor gene (AgB/1). The phylogenetic analyses revealed several ambiguities, indicating that the taxonomic status of the E. granulosus horse strain should be revised.

Animals↗
PubMedDate not supplied

Two AGAMOUS-like MADS-box genes from Taihangia rupestris (Rosaceae) reveal independent trajectories in the evolution of class C and class D floral homeotic functions.

Duplicate genes may be retained by sub- and/or neofunctionalization through changes in gene expression and/or coding sequence, and therefore have the potential to contribute to the genetic robustness and diversification of an organism. In this study, two MADS-box genes were isolated from Taihangia rupestris, a core eudicot species belonging to the Rosaceae. Sequence and phylogenetic analyses revealed that they are clade members of the euAG and PLE lineages, respectively, and hence the two genes are named TrAG (Taihangia rupestris AGAMOUS) and TrSHP (Taihangia rupestris SHATTERPROOF). Southern blot analysis shows that TrSHP is a single-copy gene in the T. rupestris genome. In situ hybridization analyses show that both TrAG and TrSHP are mainly expressed in the stamens, carpels, and ovules. When the stamen primordia are firstly observed, TrAG is initially expressed in the floral meristem domain that will initiate stamens and carpels. In contrast, no TrSHP signal is observed at this developmental stage. At late stages of carpel development, TrAG expression is detected in the ovules, ovaries, and developing styles and stigmas, whereas TrSHP expression is tightly restricted to the ovules. The transgenic Arabidopsis plants containing 35S::TrAG and 35S::TrSHP, respectively, showed similar phenotypes, including homeotic conversions of sepals into carpelloid structures bearing ovules and petals into staminoid organs, and the fruits shattering prematurely along the dehiscence zone. In addition, the phenotype of the transgenic 35S::TrSHP Arabidopsis plants revealed that perianth abscission was inhibited. Yeast two-hybrid assays indicated that TrAG can interact with TrSEP3, whereas TrSHP cannot. The data suggest that the euAG and PLE paralogs, TrAG and TrSHP, may have subfunctionalized and/or neofunctionalized through changes in expression patterns and accumulating variations in the coding regions. Taking these findings together with those available expression and functional data from Arabidopsis and other species, we conclude that the compensatory ways vary among the euAG and PLE lineage pairs in eudicot species.

Blotting, Southern↗
PubMed1980

Nucleotide sequence of genes coding for tRNAPhe and tRNATyr from a repeating unit of X. laevis DNA.

A cloned 3.18 kb repeating unit of Xenopus laevis DNA, known to contain two tRNA1Met genes, has been partially sequenced. The sequenced region could potentially code for two more tRNA species. One is a phenylalanine tRNA with the same primary sequence as that found in a variety of mammals. The other is a tyrosine tRNA with a 13 bp intervening sequence located immediately adjacent or very close to the 3' nucleotide of the anticodon. The two putative genes have opposite polarity and the sequences encoding the 5' nucleotides of the mature tRNAs are separated by only 72 bp of DNA. Homologous GC-rich sequences of dyad symmetry precede each gene. Neither gene codes for the 3' terminal CCA expected in the nature tRNAs. A short T cluster is present in the noncoding strand 3 bp away from the 3' end of the tRNATyr gene. A similar short T cluster is located 26 bp downstream of the tRNAPhe sequence. The nucleotides in between are very GC-rich and are capable of forming a stable RNA hairpin. The possible significance of these features for tRNA gene evolution, RNA splicing and transcription is discussed.

Animals↗
PubMed2005

The evolution of signaling complexity suggests a mechanism for reducing the genomic search space in human association studies.

The size complexity of the human genome has been traditionally viewed as an obstacle that frustrates efforts aimed at identifying the genetic correlates of complex human phenotypes. As such complex phenotypes are attributed to the combined action of numerous genomic loci, attempts to identify the underlying multi-locus interactions may produce a combinatorial sum of false positives that drown out the real signal. Faced with such grim prospects for successfully identifying the genetic basis of complex phenotypes, many geneticists simply disregard epistatic interactions altogether. However, the emerging picture from systems biology is that the cellular programs encoded by the genome utilize nested signaling hierarchies to integrate a number of loosely coupled, semiautonomous, and functionally distinct genetic networks. The current view of these modules is that connections encoding inter-module signaling are relatively sparse, while the gene-to-gene (protein-to-protein) interactions within a particular module are typically denser. We believe that each of these modules is encoded by a finite set of discontinuous, sequence-specific, genomic intervals that are functionally linked to association rules, which correlate directly to features in the environment. Furthermore, because these environmental association rules have evolved incrementally over time, we explore theoretical models of cellular evolution to better understand the role of evolution in genomic complexity. Specifically, we present a conceptual framework for (1) reducing genomic complexity by partitioning the genome into subsets composed of functionally distinct genetic modules and (2) improving the selection of coding region SNPs, which results in an increased probability of identifying functionally relevant SNPs. Additionally, we introduce the notion of 'genomic closure,' which provides a quantitative measure of how functionally insulated a specific genetic module might be from the influence of the rest of the genome. We suggest that the development and use of theoretical models can provide insight into the nature of biological systems and may lead to significant improvements in computational algorithms designed to reduce the complexity of the human genome.

Epistasis, Genetic↗
PubMed2002

Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria).

Mitochondrial genes have been used extensively in population genetic and phylogeographical analyses, in part due to a high rate of nucleotide substitution in animal mitochondrial DNA (mtDNA). Nucleotide sequences of anthozoan mitochondrial genes, however, are virtually invariant among conspecifics, even at third codon positions of protein-coding sequences. Hence, mtDNA markers are of limited use for population-level studies in these organisms. Mitochondrial gene sequence divergence among anthozoan species is also low relative to that exhibited in other animals, although higher level relationships can be resolved with these markers. Substitution rates in anthozoan nuclear genes are much higher than in mitochondrial genes, whereas nuclear genes in other metazoans usually evolve more slowly than, or similar to, mitochondrial genes. Although several mechanisms accounting for a slow rate of sequence evolution have been proposed, there is not yet a definitive explanation for this observation. Slow evolution and unique characteristics may be common in primitive metazoans, suggesting that patterns of mtDNA evolution in these organisms differ from that in other animal systems.

Animals↗