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PubMed2006

Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria.

The cpmA gene mediates an output signal in the cyanobacterial circadian system. This gene and its homologues are evolutionarily old, and occur in some non-photosynthetic bacteria and archaea as well as in cyanobacteria. The gene has two functional domains that differ drastically in their level of polymorphism: the N-terminal domain is much more variable than the PurE homologous C-terminal domain. The phylogenetic tree of the cpmA homologues features four main clades (C1-C4), two of which (C1 and C3) belong to cyanobacteria. These cyanobacterial clades match respective ones in the previously reported phylogenetic trees of the other genes involved in the circadian system. The phylogenetic analysis suggested that the C3 subfamily, which comprises the genes from the cyanobacteria with the kaiBC-based circadian system, experienced a lateral transfer, probably from evolutionarily old proteobacteria about 1,000 million years ago. The genes of this subfamily have a significantly higher nonsynonymous substitution rate than those of C1 (2.13 x 10(-10) and 1.53 x 10(-10) substitutions per nonsynonymous site per year, respectively). It appears that the functional and selective constraints of the kaiABC-based system have slowed down the rate of sequence evolution compared to the cpmA homologues of the kaiBC-based system. On the other hand, the differences in the mutation rates between the two cyanobacterial clades point to the different functional constraints of the systems with or without kaiA.

Bacterial Proteins↗

PubMed2001

The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA.

We describe the complete sequence of the 16,596-nucleotide mitochondrial genome of the zebrafish (Danio rerio); contained are 13 protein genes, 22 tRNAs, 2 rRNAs, and a noncoding control region. Codon usage in protein genes is generally biased toward the available tRNA species but also reflects strand-specific nucleotide frequencies. For 19 of the 20 amino acids, the most frequently used codon ends in either A or C, with A preferred over C for fourfold degenerate codons (the lone exception was AUG: methionine). We show that rates of sequence evolution vary nearly as much within vertebrate classes as between them, yet nucleotide and amino acid composition show directional evolutionary trends, including marked differences between mammals and all other taxa. Birds showed similar compositional characteristics to the other nonmammalian taxa, indicating that the evolutionary trend in mammals is not solely due to metabolic rate and thermoregulatory factors. Complete mitochondrial genomes provide a large character base for phylogenetic analysis and may provide for robust estimates of phylogeny. Phylogenetic analysis of zebrafish and 35 other taxa based on all protein-coding genes produced trees largely, but not completely, consistent with conventional views of vertebrate evolution. It appears that even with such a large number of nucleotide characters (11,592), limited taxon sampling can lead to problems associated with extensive evolution on long phyletic branches.

Animals↗

PubMed2006

The influence of environmental factors, the pollen : ovule ratio and seed bank persistence on molecular evolutionary rates in plants.

One of the main goals of molecular evolutionary biology is to determine the factors that influence the evolutionary rate of selectively neutral DNA, but much remains unknown, especially for plants. Key factors that could alter the mutation rate include environmental tolerances (because they reflect a plants vulnerability to changes in habitat), the pollen:ovule ratio (as it is associated with the number of mitotic divisions) and seed longevity (because this influences the number of generations per unit time in plants). This is the first study to demonstrate that seed bank persistence and drought tolerance are positively associated with molecular evolutionary rates in plants and that pollen:ovule ratio, shade tolerance and salinity tolerance have no detectable relationship. The implications of the findings to our understanding of the impact of environmental agents, the number of cell divisions and cell aging on neutral DNA sequence evolution are discussed.

Disasters↗

PubMed2007

Variation of estimates of SNP and haplotype diversity and linkage disequilibrium in samples from the same population due to experimental and evolutionary sample size.

Studies of genetic polymorphisms and diversity between and within human populations are increasingly characterised by a very large number of genetic markers but using a relatively small number of individuals from which DNA samples were taken. In this report we examine the limitations of a small experimental sample size relative to a large genomic sample size, and quantify the sampling variance of a number of measures of diversity and linkage disequilibrium. The relationship between sample size and observed levels of polymorphism and haplotype diversity at the level of a gene is investigated under a neutral model of sequence evolution, using coalescent simulations. It is shown that the effect of evolutionary sampling, as manifested by differences between samples (genes) in measures of diversity estimated using very large sample sizes, is substantial, with a coefficient of variation of the number of detected polymorphic SNPs or haplotypes in the order of 15%. The effect of experimental design (sample size) is also very large, and a number of 'significant' results reported in the literature can be explained by sampling alone. The expected correlation coefficient of measures of linkage disequilibrium across samples from the same population has been quantified and found to be consistent with empirical estimates from the literature.

Chromosomes, Human↗

PubMed1985

Scanning electron microscopy of normal human corneal epithelium obtained by scraping-off in vivo.

The surface of normal human corneal epithelium was examined by scanning electron microscopy (SEM). The study was carried out on specimens obtained by scraping-off in vivo, and immediately fixed. Four different types of microprojections were observed on the epithelial surface: microridges, microvilli, tufted microvilli and knobs. Detailed high magnification of surface microprojections showed that they consist of subunits. Our data suggest a correlation between surface morphology and maturity of the corneal epithelial cell. An evolutive sequence is proposed, from the youngest cell, provided with microridges, to the oldest exfoliating one, with knobs.

Cornea↗

PubMed2006

Gene transposition as a cause of hybrid sterility in Drosophila.

We describe reproductive isolation caused by a gene transposition. In certain Drosophila melanogaster-D. simulans hybrids, hybrid male sterility is caused by the lack of a single-copy gene essential for male fertility, JYAlpha. This gene is located on the fourth chromosome of D. melanogaster but on the third chromosome of D. simulans. Genomic and molecular analyses show that JYAlpha transposed to the third chromosome during the evolutionary history of the D. simulans lineage. Because of this transposition, a fraction of hybrids completely lack JYAlpha and are sterile, representing reproductive isolation without sequence evolution.

Animals↗

PubMed1989

Chromosomal location and evolutionary rate variation in enterobacterial genes.

The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.

Bias↗

PubMed1996

Asymmetries generated by transcription-coupled repair in enterobacterial genes.

Although certain replication errors occur at different frequencies on each of the complementary strands of DNA, it remains unclear whether this bias is prevalent enough during chromosome replication to affect sequence evolution. Here, nucleotide substitutions in enteric bacteria were examined, and no difference in mutation rates was detected between the leading and lagging strands, but in comparing the coding and noncoding strands, and excess of C-->T changes was observed on the coding strand. This asymmetry is best explained by transcription-coupled repair on the noncoding strand. Although the vast majority of mutations are thought to arise from spontaneous errors during replication, this result implicates DNA damage as a substantial source of mutations in the wild.

Chromosome Mapping↗

PubMed2003

Comparative study using type strains and clinical and food isolates to examine hemolytic activity and occurrence of the cyl operon in enterococci.

The hemolytic ability, the presence of cyl genes, and the diagnostic accuracy of cytolysin molecular detection were investigated in the genus Enterococcus by using 164 strains from 20 different species (26 reference strains, 42 clinical isolates from human and veterinary origin, and 96 isolates from ewe cheese and milk). Hemolysis was assayed with sheep and horse erythrocytes and under aerobic or anaerobic conditions. Screening of cytolysin genes (cylL(L), cylL(S), cylM, cylB, and cylA) was performed with new specific primers and the anaerobic assay of beta-hemolysis was used as the "gold standard" for the evaluation of cyl gene-based PCRs. Since beta-hemolysis and cyl genes were found in 10 and 14 species, respectively, the hemolytic ability seems to be spread throughout the genus ENTEROCOCCUS: Beta-hemolysis was observed in 6 of 26 (23%) reference strains, 14 of 42 (33%) clinical isolates, and 6 of 96 (6%) food isolates. The presence of cyl genes was detected in 15 of 26 (58%) reference strains, 37 of 42 (88%) clinical isolates, and 67 of 96 (70%) food isolates. These data indicate a virulence potential in food isolates, reinforcing the need of their safety assessment. Analysis of phenotypic-genotypic congruence suggests a divergent sequence evolution of cyl genes and the effect of environmental factors in the regulation of cytolysin expression. Evaluation of the diagnostic accuracy of cytolysin molecular detection points to cylL(L)-based PCR and cylL(L)L(S)MBA-based PCR as the most reliable approaches. Nevertheless, the low sensitivity (46%) and gene variability indicated by our study strongly recommend the phenotypic assay for the assessment of hemolytic ability in enterococci, followed by the molecular screening of cyl genes in nonhemolytic strains to evaluate their virulence potential.

Animals↗

PubMed2003

Dual pressure from antiretroviral therapy and cell-mediated immune response on the human immunodeficiency virus type 1 protease gene.

Human immunodeficiency virus (HIV)-specific CD8(+) T-lymphocyte pressure can lead to the development of viral escape mutants, with consequent loss of immune control. Antiretroviral drugs also exert selection pressures on HIV, leading to the emergence of drug resistance mutations and increased levels of viral replication. We have determined a minimal epitope of HIV protease, amino acids 76 to 84, towards which a CD8(+) T-lymphocyte response is directed. This epitope, which is HLA-A2 restricted, includes two amino acids that commonly mutate (V82A and I84V) in the face of protease inhibitor therapy. Among 29 HIV-infected patients who were treated with protease inhibitors and who had developed resistance to these drugs, we show that the wild-type PR82V(76-84) epitope is commonly recognized by cytotoxic T lymphocytes (CTL) in HLA-A2-positive patients and that the CTL directed to this epitope are of high avidity. In contrast, the mutant PR82A(76-84) epitope is generally not recognized by wild-type-specific CTL, or when recognized it is of low to moderate avidity, suggesting that the protease inhibitor-selected V82A mutation acts both as a CTL and protease inhibitor escape mutant. Paradoxically, the absence of a mutation at position 82 was associated with the presence of a high-avidity CD8(+) T-cell response to the wild-type virus sequence. Our results indicate that both HIV type 1-specific CD8(+) T cells and antiretroviral drugs provide complex pressures on the same amino acid sequence of the HIV protease gene and, thus, can influence viral sequence evolution.

Antiretroviral Therapy, Highly Active↗

PubMed2003

The contribution of monocyte infection and trafficking to viral persistence, and maintenance of the viral reservoir in HIV infection.

Cellular viral reservoirs and anatomic sanctuary sites allow continuing HIV-1 replication in patients with suppressed plasma viremia who are receiving highly active antiretroviral therapy and prevent eradication of HIV-1 by these regimens. Cells of macrophage lineage, including monocytes subsets within the blood, play a role in HIV-1 persistence. Evidence of sequence evolution in blood monocytes, in comparison to resting CD4+ T cells, demonstrates their distinct contribution to plasma viremia. There is evidence to suggest that a specific monocyte subset, of CD14loCD16hi phenotype, is more susceptible to HIV-1 infection than the majority of blood monocytes. Trafficking of monocytes through various tissues following their emigration from the bloodstream allows these cells to differentiate into tissue macrophages, or potentially to egress from the tissues as migratory dendritic cells. This review provides an evaluation of the contribution of monocytes to HIV-1 persistence and the HIV-1 reservoir, essential for the effective design of therapeutic eradication strategies.

Antiretroviral Therapy, Highly Active↗

PubMedDate not supplied

Rapid identification of Bordetella pertussis pertactin gene variants using LightCycler real-time polymerase chain reaction combined with melting curve analysis and gel electrophoresis.

Recently, eight allelic variants of the pertactin gene (prn1-8) have been characterized in Bordetella pertussis strains isolated in Europe and the United States. It has been suggested that the divergence of the pertactin types of clinical isolates from those of the B. pertussis vaccine strains is a result of vaccine-driven evolution. Sequencing of the prn, which is relatively time-consuming, has so far been the only method for the differentiation of prn types. We have developed a rapid real-time polymerase chain reaction assay suitable for large-scale screening of the prn type of the circulating strains. This method correctly identified the prn type of all tested 41 clinical isolates and two Finnish vaccine strains. The method is simple and reliable and provides an alternative for sequencing in pertussis research.

Amino Acid Sequence↗

PubMed2000

Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites.

Markov-process models of codon substitution were implemented that account for features of DNA sequence evolution (such as transition/transversion bias and codon usage bias) as well as heterogeneity of amino acid substitution pattern over sites. The codon (amino acid) sites are assumed to come from several classes (such as secondary structure categories), among which the rate of amino acid substitution and the effect of amino acid chemical properties vary. Parameters are estimated by the maximum likelihood method, which accounts for the phylogenetic relationship among species and corrects for multiple hits at the same site. The likelihood ratio test is used to compare models. Mitochondrial cytochrome b genes of 28 primate species are analyzed. The site-heterogeneity models provide much better fit to previous homogeneous models.

Amino Acid Substitution↗

PubMed2002

Folding pattern recognition in proteins using spectral analysis methods.

Divergence in sequence through evolution precludes sequence alignment based homology methodologies for protein folding prediction from detecting structural and folding similarities for distantly related protein. Homolog coverage of actual data bases is also a factor playing a critical role in the performance of those methodologies, the factor being conspicuously apparent in what is called the twilight zone of sequence homology in which proteins of high degree of similarity in both biological function and structure are found but for which the amino acid sequence homology ranges from about 20% to less than 30%. In contrast to these methodologies a strategy is proposed here based on a different concept of sequence homology. This concept is derived from a periodicity analysis of the physicochemical properties of the residues constituting proteins primary structures. The analysis is performed using a front-end processing technique in automatic speech recognition by means of which the cepstrum (measure of the periodic wiggliness of a frequency response) is computed that leads to a spectral envelope that depicts the subtle periodicity in physicochemical characteristics of the sequence. Homology in sequences is then derived by alignment of spectral envelopes. Proteins sharing common folding patterns and biological function but low sequence homology can then be detected by the similarity in spectral dimension. The methodology applied to protein folding recognition underscores in many cases other methodologies in the twilight zone.

Algorithms↗

PubMed2003

[Cloning and expression in E.coli of Chlamydomonas reinhardtii CrFtsZ3 gene].

FtsZ protein plays a key role in the division of bacteria and chloroplast. To investigate the evolution of the chloroplast dividing apparatus, cloning and molecular characterization of a second chloroplast division gene, CrFtsZ3, from Chlamydomonas reinhardtii is performed. As there are two ftsZ genes in Chlamydomonas reinhardtii, duplication and divergence of the ftsZ genes might occur in an early stage before the emergence of green algae during the course of plant evolution. Sequence analysis showed that CrFtsZ3 gene had significant sequence homology with other ftsZs. It encoded a precursor of 479 amino acid residues with a putative transit peptide in its N-terminal. To study the function of CrFtsZ3, a recombinant plasmid expressing the full length CrFtsZ3/EGFP fusion protein was constructed. By using IPTG inducing, overexpression of CrFtsZ3/EGFP in E.coli was achieved, and this overexpression blocked cell division and resulted in filament formation. GFP-derived fluorescence showed regularly spaced dots along the bacterial filaments. This suggests that CrFtsZ3 could still recognize the signals of cell division site in E.coli and could take part in the process of bacterial division.

Algal Proteins↗

PubMed1993

Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression.

Comparison of nucleotide sequences from different classes of vertebrates that diverged more than 300 million years ago, revealed the existence of highly conserved regions (HCRs) with more than 70% similarity over 100 to 1450 nt in non-coding parts of genes. Such a conservation is unexpected because it is much longer and stronger than what is necessary for specifying the binding of a regulatory protein. HCRs are relatively frequent, particularly in genes that are essential to cell life. In multigene families, conserved regions are specific of each isotype and are probably involved in the control of their specific pattern of expression. Studying HCRs distribution within genes showed that functional constraints are generally much stronger in 3'-non-coding regions than in promoters or introns. The 3'-HCRs are particularly A + T-rich and are always located in the transcribed untranslated regions of genes, which suggests that they are involved in post-transcriptional processes. However, current knowledge of mechanisms that regulate mRNA export, localisation, translation, or degradation is not sufficient to explain the strong functional constraints that we have characterised.

Animals↗

PubMed1997

Evolution of repeated sequence arrays in the D-loop region of bat mitochondrial DNA.

Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, theta and pi, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.

Animals↗

PubMedDate not supplied

[The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution].

The sequence analysis of proteins and mitochondrial tRNA indicated that substitutions inducing the pathogenesis in humans often occur in normal individuals of other species having no signs of pathology. The analysis of the structural stability of the protein and tRNA molecules showed that the harmful effect of pathogenic substitutions is often neutralized by other compensatory substitutions, which restore the required normal stability of the structure. A further study of this phenomenon will probably lead to new methods of treatment of genetic pathology, which would be based not on the correction of one substitution but on the correction of the stability of the molecule as an entire functional unit.

Animals↗