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At least 451 records · Page 25Linked to original sources
PubMed1998

Lampetra fluviatilis neurotrophin homolog, descendant of a neurotrophin ancestor, discloses the early molecular evolution of neurotrophins in the vertebrate subphylum.

We have isolated a neurotrophin from the lamprey that permitted us to perform a phylogenetic analysis of the neurotrophin gene family that dates back more than 460 million years to the early vertebrate ancestors. The results show that the neurotrophin gene family was originally formed by two subsequent duplications. The duplication that formed nerve growth factor, neurotrophin-3, brain-derived neurotrophic factor, and neurotrophin-4/5 occurred after the split of lampreys but before the split of cartilaginous fish from the main vertebrate lineage. Compilation of chromosomal gene maps around the neurotrophins shows that they are located in paralogous regions, suggesting that the genes were formed at major duplication events possibly by complete genome doubling. Analysis of two isolated Trk receptor sequences shows similar results as for the lamprey neurotrophin. Multiple neurotrophin and Trk genes, including neurotrophin-6 and -7, have been found in bony fish, and we suggest that the extra genes were formed by an additional duplication in the bony fish lineage. Analysis of lamprey Trk mRNA expression in the adult brain shows that the genes are expressed in all regions analyzed so far. Together, the results suggest that the duplications of ancestral neurotrophin and Trk genes at an early vertebrate stage have permitted evolution to bring about differential neurotrophin and Trk expression, thereby allowing the formation of specific functions in selective neuronal populations.

Amino Acid Sequence↗
PubMed2002

Rates and patterns of molecular evolution in inbred and outbred Arabidopsis.

The evolution of self-fertilization is associated with a large reduction in the effective rate of recombination and a corresponding decline in effective population size. If many spontaneous mutations are slightly deleterious, this shift in the breeding system is expected to lead to a reduced efficacy of natural selection and genome-wide changes in the rates of molecular evolution. Here, we investigate the effects of the breeding system on molecular evolution in the highly self-fertilizing plant Arabidopsis thaliana by comparing its coding and noncoding genomic regions with those of its close outcrossing relative, the self-incompatible A. lyrata. More distantly related species in the Brassicaceae are used as outgroups to polarize the substitutions along each lineage. In contrast to expectations, no significant difference in the rates of protein evolution is observed between selfing and outcrossing Arabidopsis species. Similarly, no consistent overall difference in codon bias is observed between the species, although for low-biased genes A. lyrata shows significantly higher major codon usage. There is also evidence of intron size evolution in A. thaliana, which has consistently smaller introns than its outcrossing congener, potentially reflecting directional selection on intron size. The results are discussed in the context of heterogeneity in selection coefficients across loci and the effects of life history and population structure on rates of molecular evolution. Using estimates of substitution rates in coding regions and approximate estimates of divergence and generation times, the genomic deleterious mutation rate (U) for amino acid substitutions in Arabidopsis is estimated to be approximately 0.2-0.6 per generation.

Arabidopsis↗
PubMed1995

A short introduction to the origin and molecular evolution of viruses.

The present review deals with conceptual and experimental approaches to two aspects of the origin and molecular evolution of viruses. In the section "Role of Retrons, Retroelements, and Reverse Transcriptase in the Evolution of Retroviruses and in Eukaryotic Genome Plasticity", Temin's concept that retrons are an ancient genetic element that during evolution of the species gave rise to retroviruses is presented. An opposing view of Xiong and Eickbush that the most probable ancestor of current retroelements is a retrotransposable element with gag- and pol-like genes is presented. Minus-strand RNA viruses are also discussed. The second aspect of this review is the molecular evolution of viruses at the level of the virus genome. Spiegelman's experiment on the evolution of self-replicating nucleic acid molecules outside living cells and Eigen's experimental and conceptual approaches to this subject are presented, along with studies on the evolutionary rates of base substitutions in viral RNA and defective molecules generated during replication.

Animals↗
PubMed2003

Molecular evolution of a plastid tandem repeat locus in an orchid lineage.

The molecular evolution of a chloroplast minisatellite locus in the Anacamptis palustris (Orchidaceae) lineage and haplotype variation in two Italian A. palustris populations were investigated. A phylogenetic analyses of the chloroplast tRNA(LEU) intron, where the minisatellite locus is located, revealed that a deletion in the ancestor of the A. palustris lineage led to the formation of two noncontiguous, complementary sequence motifs. We propose a model to explain the initial formation of the minisatellite repeat motif, starting with the two noncontiguous, complementary sequence motifs. A survey of minisatellite variation in four species of the A. palustris lineage revealed several haplotypes that differed not only in repeat number, but also in repeat organization. A haplotype network suggests that three different minisatellite loci evolved independently at the same position in the tRNA(LEU) intron. A secondary structure model revealed that the A. palustris minisatellite repeat forms a stem region of the tRNA(LEU) intron, which allows its notable expansion without negatively affecting splicing. Minisatellite variation was high in the two examined A. palustris populations where 20 haplotypes were detected, whereas no length variation was detected in a neighboring poly (A) microsatellite locus. We estimated a chloroplast minisatellite mutation rate of 3.2 x 10(-3) mutations per generation. Southern blot analyses did not find evidence for chloroplast heteroplasmy. Based on the analysis of the largest known, extant A. palustris population, a stepwise mutation model (SMM) was inferred.

Evolution, Molecular↗
PubMed2004

Molecular evolution of the trnTUGU-trnFGAA region in Bryophytes.

Structure, variability, and molecular evolution of the trnT-F region in the Bryophyta (mosses and liverworts) is analyzed based on about 200 sequences of the trnT-L spacer and trnL 5' exon, 1000 sequences of the trnL intron, and 800 sequences of the trnL 3' exon and trnL-F spacer, including comparisons of lengths, GC contents, sequence similarities, and functional elements. Mutations occurring in the trnL 5' and 3' exons, including compensatory base pair changes, and a transition in the trnL anticodon in Takakia lepidozioides, are discussed. All three non-coding regions display a mosaic structure of highly variable elements (V1 - V3 in the trnT-L spacer, V4/V5 corresponding to stem-loop regions P6/P8 in the trnL intron, and V6/V7 in the trnL-F spacer) and more conserved elements. In the trnL intron this structure is a consequence of the defined secondary structure necessary for correct splicing, whereas in both spacers conserved regions are restricted to promoter elements. At least the highly variable regions in the trnT-L spacer and stem-loop region P8 of the trnL intron seem to evolve independently in the major bryophyte lineages and are therefore not suitable for high taxonomic level phylogenetic reconstructions. In mosses, a trend of length reduction towards the more derived lineages is observed in all three non-coding regions. GC contents are mostly linked to sequence variability, with the conserved regions being more GC rich and the more variable AT rich. The lowest GC values (< 10 %) are found in the trnT-L spacer of mosses. In addition to two putative sigma (70)-type promoters in the trnT-L spacer, a third putative promoter is present in the trnL-F spacer, although trnL and trnF are assumed to be co-transcribed. Consensus sequences are provided for the -35 and -10 sequences of the major bryophyte lineages. The third promoter is part of a hairpin secondary structure, whose loop region is highly homoplastic in mosses due to an inversion occurring independently in non-related taxa, even at the intraspecific level.

Base Sequence↗
PubMed1998

[Different patterns of molecular evolution of influenza A viruses in avian and human population].

Patterns of molecular evolution of the influenza virus proteins and genes are discussed. The subsets of all viral genes corresponding to statistically significant clusters on dendrogram were shown to fall into two distinct groups. The first group was characterized by the presence of an exact linear relationship between the year of the strain isolation and the evolutionary distance. The subsets of human influenza virus genes belong to this group. A method for eliminating the "frozen" strains from the subsets and for calculating the evolutionary rates without construction of phylogenetic trees has been elaborated. The substitution rates calculated according to this technique agreed with the data obtained previously. A linear relationship was not observed in the second group. This group was predominantly composed of avian influenza virus genes. The lack of linear correlation pointed to the cocirculation of a large amount of different influenza virus genomic segments in the avian population. An approach for an examination of the role of intragenic recombination in the development of the antigenic subtypes of hemagglutinin is suggested. Our results suggest that recombination did not play a considerable role in this process, and that all modern subtypes of this protein were probably formed before the introduction of the influenza viruses into the human population. These findings are consistent with the hypothesis that influenza viruses penetrated into human population from their pools in avian populations.

Animals↗
PubMed1981

Stepwise molecular evolution of bacterial photosynthetic energy conversion.

The concept of continuity in molecular evolution implies a stepwise formation of metabolic systems and processes. In this manner, chemical and biological evolution have given rise, step by step, to such complicated systems as the photosynthetic apparatus and thus, such elaborate processes as photosynthesis in the living cell. Among currently living organisms, the bacteria contain a much less complex photosynthetic system than the algae and higher plants, which uniquely are capable fo splitting H2O. But also the bacterial system is a very highly evolved and sophisticated, membrane-bound apparatus for the transformation of light energy to other biologically useful energy forms. The study of its molecular evolution is here undertaken by the method of attempting to break down the system into its main components and functions in order to elucidate how they had originated and evolved, and how, by divergent and convergent evolutionary steps, the stage was set for the arrival of bacterial photophosphorylation.

Adenosine Triphosphatases↗
PubMed2000

The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.

The pyridoxal-5-phosphate-dependent enzymes (B6 enzymes) that act on amino acid substrates are of multiple evolutionary origin. The numerous common mechanistic features of B6 enzymes thus are not historical traits passed on from a common ancestor enzyme but rather reflect evolutionary or chemical necessities. Family profile analysis of amino acid sequences supported by comparison of the available three-dimensional (3-D) crystal structures indicates that the B6 enzymes known to date belong to four independent evolutionary lineages of homologous (or more precisely paralogous) proteins, of which the alpha family is by far the largest. The alpha family (with aspartate aminotransferase as the prototype enzyme) includes enzymes that catalyze, with several exceptions, transformations of amino acids in which the covalency changes are limited to the same carbon atom that carries the amino group forming the imine linkage with the coenzyme (i.e., Calpha in most cases). Enzymes of the beta family (tryptophan synthase beta as the prototype enzyme) mainly catalyze replacement and elimination reactions at Cbeta. The D-alanine aminotransferase family and the alanine racemase family are the two other independent lineages, both with relatively few member enzymes. The primordial pyridoxal-5-phosphate-dependent enzymes apparently were regio-specific catalysts that first diverged into reaction-specific enzymes and then specialized for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages. Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts. In attempts to stimulate particular steps of molecular evolution, oligonucleotide-directed mutagenesis of active-site residues and directed molecular evolution have been applied to change both the substrate and reaction specificity of existent B6 enzymes. Pyridoxal-5-phosphate-dependent catalytic antibodies were elicited with a screening protocol that applied functional selection criteria as they might have been operative in the evolution of protein-assisted pyridoxal catalysis.

Alanine Racemase↗
PubMed1994

Evolution of glutamine synthetase genes is in accordance with the neutral theory of molecular evolution.

Evolution of glutamine synthetase gene is discussed on the results of DNA sequence analysis of the gene. Thirty DNA sequences of various organisms spanning from prokaryotes to eukaryotes were collected from the DNA data banks and translated first, they were aligned next, then evolutionary distances were computed, and molecular phylogeny was finally estimated. The results of the alignment reveal that functionally important regions of glutamine synthetase have been evolutionarily more conserved than the remaining regions. The evolutionary distances computed also show that the rate of synonymous substitution is higher than that of nonsynonymous substitution. These are well in accordance with the neutral theory of molecular evolution. Besides, the molecular phylogeny obtained shows that the origin of glutamine synthetase gene is much earlier than the divergence between eukaryotes and prokaryotes, suggesting that the gene is one of the oldest genes functioning now.

Amino Acid Sequence↗
PubMed2003

Molecular evolution meets the genomics revolution.

Changes in technology in the past decade have had such an impact on the way that molecular evolution research is done that it is difficult now to imagine working in a world without genomics or the Internet. In 1992, GenBank was less than a hundredth of its current size and was updated every three months on a huge spool of tape. Homology searches took 30 minutes and rarely found a hit. Now it is difficult to find sequences with only a few homologs to use as examples for teaching bioinformatics. For molecular evolution researchers, the genomics revolution has showered us with raw data and the information revolution has given us the wherewithal to analyze it. In broad terms, the most significant outcome from these changes has been our newfound ability to examine the evolution of genomes as a whole, enabling us to infer genome-wide evolutionary patterns and to identify subsets of genes whose evolution has been in some way atypical.

Animals↗
PubMed1998

Molecular evolution modeled as a fractal Poisson process in agreement with mammalian sequence comparisons.

The fractal doubly stochastic Poisson process (FDSPP) model of molecular evolution, like other doubly stochastic Poisson models, agrees with the high estimates for the index of dispersion found from sequence comparisons. Unlike certain previous models, the FDSPP also predicts a positive geometric correlation between the index of dispersion and the mean number of substitutions. Such a relationship is statistically proven herein using comparisons between 49 mammalian genes. There is no characteristic rate associated with molecular evolution according to this model, but there is a scaling relationship in rates according to a fractal dimension of evolution. The FDSPP is a suitable replacement for the homogeneous Poisson process in tests of the lineage dependence of rates and in estimating confidence intervals for divergence times. As opposed to other fractal models, this model can be interpreted in terms of Darwinian selection and drift.

Animals↗
PubMed2000

Directed molecular evolution of cytochrome c peroxidase.

Cytochrome c peroxidase (CCP) from Saccharomyces cerevisiae was subjected to directed molecular evolution to generate mutants with increased activity against the classical peroxidase substrate guaiacol, thus changing the substrate specificity of CCP from the protein cytochrome c to a small organic molecule. After three rounds of DNA shuffling and screening, mutants were isolated which possessed a 300-fold increased activity against guaiacol and an up to 1000-fold increased specificity for this substrate relative to that for the natural substrate. In all of the selected mutants, the distal arginine (Arg48), which is fully conserved in the superfamily of peroxidases, was mutated to histidine, showing that this mutation plays a key role in the significant increase in activity against phenolic substrates. The results suggest that, in addition to stabilizing the reactive intermediate compound I, the distal arginine plays an important role as a gatekeeper in the active site of CCP, controlling the access to the ferryl oxygen and the distal histidine. Other isolated mutations increase the general reactivity of the peroxidase or increase the intracellular concentration of the active holo form, allowing their selection under the employed screening conditions. The results illustrate the ability of directed molecular evolution technologies to deliver solutions to biochemical problems that would not be readily predicted by rational design.

Alanine↗
PubMed2004

PyEvolve: a toolkit for statistical modelling of molecular evolution.

BACKGROUND: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. RESULTS: Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. CONCLUSION: PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Animals↗
PubMed2000

Molecular evolution of the histone 3 multigene family in the Drosophila melanogaster species subgroup.

Molecular evolution of the histone multigene family was studied by cloning and sequencing regions of the histone 3 gene in the Drosophila melanogaster species subgroup. Analysis of the nucleotide substitution pattern showed that in the coding region synonymous changes occurred more frequently to A or T in contrast to the GC-rich base composition, while in the 3' region the nucleotide substitutions were most likely in equilibrium. These results suggested that the base composition at the third codon position of the H3 gene, i.e., codon usage, has been changing to A or T in the Drosophila melanogaster species subgroup.

Animals↗
PubMed2005

Increased rates of molecular evolution in an equatorial plant clade: an effect of environment or phylogenetic nonindependence?

A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent contrasts to test for an effect of environment across this entire subgenus. We find very little evidence for an effect of latitude on rate of molecular evolution using these approaches and believe that the shared evolutionary history of the clade is a plausible explanation of the apparent rate difference between equatorial and subequatorial Mearnsia species.

DNA, Plant↗