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PubMed2004

Adjusting for selection on synonymous sites in estimates of evolutionary distance.

Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relationship between codon bias and synonymous divergence observed in four species of the genus Saccharomyces to provide a simple correction for selection on silent sites.

DNA↗
PubMed2004

Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition.

Germ-line mutations in the BRCA1 gene predispose affected individuals to breast and ovarian cancer syndromes. In an attempt to systematically analyze a broader spectrum of genetic changes ranging from frequent exon deletions and duplications to amino acid replacements and protein truncations, we isolated and characterized full size BRCA1 homologues from a representative group of non-human primates. Our analysis represents the first comprehensive sequence comparison of primate BRCA1 loci and corresponding proteins. The comparison revealed an unusually high proportion of indels in non-coding DNA. The major force driving evolutionary changes in non-coding BRCA1 sequences was Alu-mediated rearrangements, including Alu transpositions and Alu-associated deletions, indicating that structural instability of this locus may be intrinsic in anthropoids. Analysis of the non-synonymous/synonymous ratio in coding portions of the gene revealed the presence of both conserved and rapidly evolving regions in the BRCA1 protein. Previously, a rapidly evolving region with evidence of positive evolutionary selection in human and chimpanzee had been identified only in exon 11. Here, we show that most of the internal BRCA1 sequence is variable between primates and evolved under positive selection. In contrast, the terminal regions of BRCA1, which encode the RING finger and BRCT domains, experienced negative selection, which left them almost identical between the compared primates. Distribution of the reported missense mutations, but not frameshift and nonsense mutations, is positively correlated with BRCA1 protein conservation. Finally, on the basis of protein sequence conservation, we identified missense changes that are likely to compromise BRCA1 function.

Alu Elements↗
PubMed2003

PAI-1 polymorphisms modulate phenotypes associated with the metabolic syndrome in obese and diabetic Caucasian population.

AIM/HYPOTHESIS: Plasminogen activator inhibitor-1 (PAI-1) is a main regulator of the endogenous fibrinolytic system and modulates the thrombosis progression. We analyzed genetic contributions of PAI-1 mutations to the metabolic syndrome and to its complications. METHODS: PAI-1 promoter and coding sequences were screened for mutations. Genotypes were determined for 1067 unrelated individuals of a French Caucasian cohort, selected for diabetes and obesity. Association between PAI-1 polymorphisms and phenotypes related to metabolic syndrome were statistically studied. RESULTS: There were five variants identified: two common polymorphisms, -765 4G/5G and -844 A>G, in the promoter, and three new non-synonymous SNPs, Ala15Thr, Val17Ile and Asn195Ile. In obese non-diabetic subjects, the two promoter polymorphisms were associated with higher fasting glucose concentrations (p=0.006 and p=0.0004, for -765 4G/5G and -844 A>G, respectively) and insulin (p=0.05 and p=0.008, for -765 4G/5G and -844 A>G, respectively). Moreover, the -844 A>G SNP was associated with lower triglyceride (p=0.002) and higher HDL cholesterol concentrations (p=0.02) in lean subjects. In addition, the two promoter and Ala15Thr polymorphisms showed a trend towards association with CHD in diabetic subjects (-765 4G/5G: 0.56/0.51, p=0.05; -844 A>G: 0.63/0.57, p=0.02; Ala15Thr: 0.91/0.88, p=0.04). The SNPs Ala15Thr, located in the PAI-1 signal peptide, and rare the Asn195Ile, located in a beta-sheet structure, could influence conformation of these two structures. CONCLUSIONS/INTERPRETATION: Our results support the hypothesis that PAI-1 polymorphisms probably interact with known environmental risk factors (chronic hyperglycaemia, obesity, etc.) to induce a more severe insulin-resistant metabolic profile in overweight subjects, and to further increase risk for CHD in diabetic subjects.

Body Mass Index↗
PubMed1997

The atypical codon usage of the plant psbA gene may be the remnant of an ancestral bias.

The psbA gene of the chloroplast genome has a codon usage that is unusual for plant chloroplast genes. In the present study the evolutionary status of this codon usage is tested by reconstructing putative ancestral psbA sequences to determine the pattern of change in codon bias during angiosperm divergence. It is shown that the codon biases of the ancestral genes are much stronger than all extant flowering plant psbA genes. This is related to previous work that demonstrated a significant increase in synonymous substitution in psbA relative to other chloroplast genes. It is suggested, based on the two lines of evidence, that the codon bias of this gene currently is not being maintained by selection. Rather, the atypical codon bias simply may be a remnant of an ancestral codon bias that now is being degraded by the mutation bias of the chloroplast genome, in other words, that the psbA gene is not at equilibrium. A model for the evolution of selective pressure on the codon usage of plant chloroplast genes is discussed.

Base Sequence↗
PubMed2007

Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.

Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.

Codon↗
PubMed1995

Nucleotide sequence analysis of recent epidemic strains of enterovirus 70.

Nucleotide sequences of the genome of enterovirus 70 (EV70) isolated in Osaka in 1993 were determined, and compared with those of the past epidemic strains. Nucleotide substitution rates in 332 bp, 174 bp, and 178 bp of the genes encoding viral protein (VP)1, VP2, or VP3 were 9.0, 7.5, and 5.6% between Kumoi-2/93 and J670/71, respectively. Likewise, the putative amino acid substitution rates were 1.8, 0, and 0%. It seems that the epidemic strains of EV70 in Japan have been evolving at a constant high nucleotide substitution rate but almost all the substitutions were synonymous.

Aged↗
PubMed1996

Glioblastoma multiforme: radiologic-pathologic correlation.

Astrocytic tumors are divided into two basic categories: circumscribed (grade I) or diffuse (grades II-IV). All diffuse astrocytomas tend to progress to grade IV astrocytoma, which is synonymous with glioblastoma multiforme (GBM). GBMs are characterized by marked neovascularity, increased mitosis, greater degree of cellularity and nuclear pleomorphism, and microscopic evidence of necrosis. Several genetic abnormalities have been associated with the development of GBM: In some cases, the abnormality is inherited (e.g., Li-Fraumeni syndrome); in others, genetic alteration appears to result from mutation into an oncogene or deterioration of the tumor-suppressor gene p53. A common, distinctive histopathologic feature of GBM is pseudopalisading. The most common imaging appearance of GBM is a large heterogeneous mass in the supratentorial white matter that exerts considerable mass effect. Less frequently, GBM can occur near the dura mater or in the corpus callosum, posterior fossa, and spinal cord. GBM typically contains central areas of necrosis, has thick irregular walls, and is surrounded by extensive, vasogenic edema, but the tumor may also have thin round walls, scant edema, or a cystic appearance with a mural nodule. GBMs most commonly metastasize from their original location by direct extension along white matter tracts; however, cerebrospinal fluid, subependymal, and hematogenous spread also can occur. Given the rapidly growing body of knowledge about GBM, the radiologist's role is more important than ever in accurate and timely diagnosis.

Aged↗
PubMed2003

Hepatitis C virus E2 and NS5A region variability during sequential treatment with two interferon-alpha preparations.

To determine the pattern and significance of the HCV genetic heterogeneity before and during treatment with recombinant-2b or lymphoblastoid alpha-interferon, hypervariable region 1 (HVR-1) and NS5A quasispecies were characterised by cloning and sequencing in 12 HCV-1b-infected subjects. Patients were either responder-relapsers or non-responders to treatment. Extensive amino acid sequence analysis was applied to reveal the significance of HCV variation at key sites within HVR-1 and NS5A regions. Genetic complexity, genetic diversity, and the non-synonymous to synonymous substitution ratios of HVR-1 quasispecies decreased during treatment in responder-relapser patients only, and more markedly so following lymphoblastoid alpha-interferon. In non-responders, the HVR-1 quasispecies broadened. Amino acids G406 and Q409, which represent a major viral epitope, were highly conserved throughout treatment. Responder-relapser patients had a higher mutation frequency in NS5A than non-responders. Lymphoblastoid alpha-interferon promoted the selection of intermediate Interferon Sensitivity Determining Region (ISDR) sequences, whereas recombinant-2b alpha-interferon favoured maintenance or selection of conserved ISDR sequences. Variability upstream of the ISDR was associated with treatment response, but the amino acid substitutions conferring higher replicative ability to in vitro HCV replicons were absent in in vivo isolates. In conclusion, the pattern of HVR-1 quasispecies evolution correlates with the clinical response, and the conservation of specific amino acids may be useful for immune targeting in vivo. In responder-relapser patients, the initial HVR-1 evolution resembles that found in sustained responders. Variability within the entire NS5A, as opposed to a single region (ISDR), may have a role in influencing alpha-interferon treatment outcome. A differential effect of different alpha-interferon preparations on HCV quasispecies kinetics may exist.

Amino Acid Sequence↗
PubMed2005

Natural selection during functional divergence to LMP7 and proteasome subunit X (PSMB5) following gene duplication.

The LMP7 and PSMB5 genes were created through an ancient gene duplication event of their ancestral locus. These proteins contain an active site of proteolysis, and LMP7 replaces PSMB5 as a component of the 20S proteasome after stimulation of cells by interferon-gamma. Replacement of PSMB5 by LMP7 changes the profile of the products of 20S proteasome processing, predisposing digested peptides for transport to and display by the immune system. The purpose of this study is to investigate evolutionary forces influencing functional divergence between LMP7 and PSMB5 following duplication. Levels of synonymous and nonsynonymous substitution rates are estimated to infer differences in levels of natural selection. Estimates of substitution rates indicate that natural selection elevated rates of nonsynonymous substitution in LMP7 following gene duplication, whereas PSMB5 experienced an increase in substitution rate that was not likely due to diversifying natural selection following duplication. Following initial divergence, nearly neutral mutations have dominated gene evolution in both lineages. The LMP7 gene locus provides a rare example of a protein with specialized function arising from duplication and divergence of a housekeeping protein by way of natural selection.

Animals↗
PubMed2005

Does radial nuclear organisation influence DNA damage?

It has been suggested that chromatin at the nuclear periphery could act to shield DNA sequences in the nuclear interior from damage. To test this hypothesis, we have examined the nuclear distribution of sites of DNA repair induced by oxidation or UV-C. We do not detect more damage (repair) at the nuclear periphery than in the nuclear interior. In fact, contrary to the body guard hypothesis, there is an excess of damage detected in the nuclear interior. This is further supported by sequence comparison between genes on human chromosomes 18 or 19, and their counterparts in the chimpanzee. The synonymous substitution rate for genes on chromosome 19, which is located towards the centre of the human nucleus, was higher than that for genes on chromosome 18, which is located at the nuclear periphery. We conclude that chromatin at the periphery of the human nucleus is not able to protect more internally located sequences from damage and mutation. We suggest that features of the chromatin structure, or base composition, of sequences in the nuclear centre make them more susceptible to damage.

Cell Line, Tumor↗
PubMed2000

Population structure and recent evolution of Plasmodium falciparum.

Plasmodium falciparum is the agent of malignant malaria, one of mankind's most severe maladies. The parasite exhibits antigenic polymorphisms that have been postulated to be ancient. We have proposed that the extant world populations of P. falciparum have derived from one single parasite, a cenancestor, within the last 5, 000-50,000 years. This inference derives from the virtual or complete absence of synonymous nucleotide polymorphisms at genes not involved in immune or drug responses. Seeking to conciliate this claim with extensive antigenic polymorphism, we first note that allele substitutions or polymorphisms can arise very rapidly, even in a single generation, in large populations subject to strong natural selection. Second, new alleles can arise not only by single-nucleotide mutations, but also by duplication/deletion of short simple-repeat DNA sequences, a process several orders of magnitude faster than single-nucleotide mutation. We analyze three antigenic genes known to be extremely polymorphic: Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes.

Amino Acid Sequence↗
PubMed2002

Evolution of Ig DNA sequence to target specific base positions within codons for somatic hypermutation.

Ig variable (V) region genes are subjected to a somatic hypermutation process as B lymphocytes participate in immune reactions to protein Ags. Although little is known regarding the mechanism of mutagenesis, a consistent hierarchy of trinucleotide target preferences is evident. Analysis of trinucleotide regional distributions predicted and we now empirically confirm the surprising finding that the framework 2 region of kappa V region genes is highly mutable despite its importance to the structural integrity and function of the Ab molecule. Interestingly, much of this mutability appears to be focused on the third codon position where synonymous substitutions are most likely to occur. We also observed a trend for high predicted mutability for codon positions 1 and 2 in complementarity-determining regions. Consequently, amino acid replacements should occur at a higher rate in complementarity-determining regions than in framework regions due to the distribution and subsequent targeting of microsequences by the mutation mechanism. Our results reveal a subtle tier of V region gene evolution in which DNA sequence has been molded to direct mutations to specific base positions within codons in a manner that minimizes damage and maximizes the benefits of the somatic hypermutation process.

Animals↗
PubMed2003

[DNA polymorphism of Drosophila genes and factors determining it].

The data on variation of DNA sequences in genes of Drosophilidae are reviewed. Intraspecific polymorphism and interspecific divergence of DNA nucleotide sequences are shown to be characteristic of most genes. The level of intraspecific polymorphism and interspecific DNA divergence and the degree of correlation between them depend on the mode, intensity, and direction of natural selection, as well as on the evolutionary history of the genes and species. The evolutionary role of synonymous and nonsynonymous nucleotide substitutions in DNA is analyzed. Genes responsible for the reproduction and genes controlling other functions are compared in respect to their variation.

Animals↗
PubMed2005

Dynamics of hepatitis C virus NS5A quasispecies during interferon and ribavirin therapy in responder and non-responder patients with genotype 1b chronic hepatitis C.

The quasispecies nature of hepatitis C virus (HCV) may have important implications concerning resistance to antiviral agents. To determine whether HCV NS5A quasispecies composition and dynamics are related to responsiveness to combined interferon (IFN) and ribavirin therapy, extensive sequence analyses of cloned RT-PCR amplification products of HCV-1b NS5A quasispecies of sequential isolates from 15 treated (nine sustained responders and six non-responders) and three untreated patients were performed. Accumulation of mutations in NS5A during therapy was relatively frequent in the V3 domain, but unusual elsewhere. Amino acid changes were the result of the imposition of minor variants that were already present before treatment and always occurred within the first week of therapy. Before treatment, the complexity and diversity of quasispecies were lower in isolates from responders than in those from non-responders, particularly in the V3 domain, where differences in nucleotide entropy (0.35 vs 0.64, P=0.003), genetic distance (0.0145 vs 0.0302, P=0.05) and non-synonymous substitutions (0.0102 vs 0.0203, P=0.036) were statistically significant. These differences became more apparent during treatment, because complexity and diversity remained stable or tended to increase in non-responders, whereas they tended to decrease in responders. These observations suggest that the composition and dynamics of HCV NS5A quasispecies, particularly in the V3 domain, may play a role in the response to combined IFN/ribavirin therapy.

Amino Acid Sequence↗
PubMed2001

Classification of the spectrum of Coats' disease as subtypes of idiopathic retinal telangiectasis with exudation.

PURPOSE: An increasing variety of eponymous terms have been used to describe atypical cases of Coats' disease. A group of typical cases of Coats' disease and other cases of differing severity were classified as one of four subtypes of idiopathic retinal telangiectasis with exudation and compared with regard to clinical outcome. METHODS: In a retrospective clinical review patients with typical and atypical Coats' disease were classified as severe, focal, juxtafoveal or associated (with another disease) forms of idiopathic retinal telangiectasis with exudation. RESULTS: 53 eyes in 50 patients were examined of which 62% (n=31) were male. 12 eyes were classified as severe (group 1), 22 focal (group 2), 12 juxtafoveal (group 3) and 7 associated (group 4). The mean age at diagnosis was lowest in group 1 eyes (6.8 years). The best visual acuity at presentation was 6/60 in group 1 whereas high proportions of eyes in the other groups had initial visual acuities of 6/24 or better. In group 1 only one eye was treated, the majority of eyes were blind or had been enucleated whereas 34 (79%) of eyes in the other groups were suitable for treatment and 29 eyes (67%) retained pre-treatment visual acuity or better at last follow-up. CONCLUSIONS: Idiopathic retinal telangiectasis with exudation is a spectrum of disease, which is synonymous with Coats' disease. In this retrospective study eyes with severe idiopathic retinal telangiectasis with exudation corresponding to typical Coats' disease, have poorer vision at presentation, are less suitable for treatment and have worse outcomes than eyes with other subtypes. The spectrum of disease severity seen in idiopathic retinal telangiectasis with exudation may be due to second somatic mutations in genes with an existing germline mutation (the two hit theory) and a mosaic phenotype.

Adolescent↗
PubMed2003

A personalized and automated dbSNP surveillance system.

The development of high throughput techniques and large-scale studies in the biological sciences has given rise to an explosive growth in both the volume and types of data available to researchers. A surveillance system that monitors data repositories and reports changes helps manage the data overload. We developed a dbSNP surveillance system (URL: http://www.pharmgkb.org/do/serve?id=tools.surveillance.dbsnp) that performs surveillance on the dbSNP database and alerts users to new information. The system is notable because it is personalized and fully automated. Each registered user has a list of genes to follow and receives notification of new entries concerning these genes. The system integrates data from dbSNP, LocusLink, PharmGKB, and Genbank to position SNPs on reference sequences and classify SNPs into categories such as synonymous and non-synonymous SNPs. The system uses data warehousing, object model-based data integration, object-oriented programming, and a platform-neutral data access mechanism.

DNA↗
PubMed2003

Mutational bias affects protein evolution in flowering plants.

Amino acid sequences from several thousand homologous gene pairs were compared for two plant genomes, Oryza sativa and Arabidopsis thaliana. The Arabidopsis genes all have similar G+C (guanine plus cytosine) contents, whereas their homologs in rice span a wide range of G+C levels. The results show that those rice genes that display increased divergence in their nucleotide composition (specifically, increased G+C content) showed a corresponding, predictable change in the amino acid compositions of the encoded proteins relative to their Arabidopsis homologs. This trend was not seen in a "control" set of rice genes that had nucleotide contents closer to their Arabidopsis homologs. In addition to showing an overall difference in the amino acid composition of the homologous proteins, we were also able to investigate the biased patterns of amino acid substitution since the divergence of these two species. We found that the amino acid exchange matrix was highly asymmetric when comparing the High G+C rice genes with their Arabidopsis homologs. Finally, we investigated the possible causes of this biased pattern of sequence evolution. Our results indicate that the biased pattern of protein evolution is the consequence, rather than the cause, of the corresponding changes in nucleotide content. In fact, there is an even more marked asymmetry in the patterns of substitution at synonymous nucleotide sites. Surprisingly, there is a very strong negative correlation between the level of nucleotide bias and the length of the coding sequences within the rice genome. This difference in gene length may provide important clues about the underlying mechanisms.

Amino Acids↗
PubMed2006

Neutral evolution of synonymous base composition in the Brassicaceae.

The GC content of synonymous sites is elevated in genes from both Brassica oleraceae and Arabidopsis lyrata compared with Arabidopsis thaliana. However, this shift in base composition is independent of gene expression level, and there is no evidence for a similar difference in the frequency of codons preferred by translational selection. The results suggest that composition evolution is caused by a change in mutation bias or biased gene conversion, rather than by a reduction in the efficacy of natural selection in selfing Arabidopsis.

Arabidopsis↗