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PubMed2002

Search for genes positively selected during primate evolution by 5'-end-sequence screening of cynomolgus monkey cDNAs.

It is possible to assess positive selection by using the ratio of K(a) (nonsynonymous substitutions per plausible nonsynonymous sites) to K(s) (synonymous substitutions per plausible synonymous sites). We have searched candidate genes positively selected during primate evolution by using 5'-end sequences of 21,302 clones derived from cynomolgus monkey (Macaca fascicularis) brain cDNA libraries. Among these candidates, 10 genes that had not been shown by previous studies to undergo positive selection exhibited a K(a)/K(s) ratio > 1. Of the 10 candidate genes we found, 5 were included in the mitochondrial respiratory enzyme complexes, suggesting that these nuclear-encoded genes coevolved with mitochondrial-encoded genes, which have high mutation rates. The products of other candidate genes consisted of a cell-surface protein, a member of the lipocalin family, a nuclear transcription factor, and hypothetical proteins.

Animals↗
PubMed2001

Origin and evolution of GBV-C/hepatitis G virus and relationships with ancient human migrations.

The GB virus C/hepatitis G virus (GBV-C/HGV) is a newly identified human RNA virus, belonging to the Flaviviridae family. Persistent infection by GBV-C/HGV is common in humans, and genetically divergent isolates have been identified in different parts of the world. Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin and evolution of GBV-C/HGV were examined using a set of fully sequenced strains of worldwide origin. A first phylogenetic analysis, addressed to the short (255 nucleotides) NS5A overlapping coding region by the neighbor-joining method, suggested an ancient African origin of GBV-C/HGV. This notion was confirmed when the same analysis was applied to the genomic regions showing the lowest rate of synonymous substitutions, covering one-fourth (2184 nucleotides) of the total coding potential of the virus genome. By using a multivariate statistical method and extending the analysis to the complete coding region, fine details of the evolutionary history of GBV-C/HGV were further elucidated. By this approach, isolates from Southeast Asia appeared to be the most closely related to those of African origin, consistent with a major route of ancient human migrations from Africa to southeastern parts of the Asian continent.

Base Sequence↗
PubMed2003

The case for an error minimizing standard genetic code.

Since discovering the pattern by which amino acids are assigned to codons within the standard genetic code, investigators have explored the idea that natural selection placed biochemically similar amino acids near to one another in coding space so as to minimize the impact of mutations and/or mistranslations. The analytical evidence to support this theory has grown in sophistication and strength over the years, and counterclaims questioning its plausibility and quantitative support have yet to transcend some significant weaknesses in their approach. These weaknesses are illustrated here by means of a simple simulation model for adaptive genetic code evolution. There remain ill explored facets of the 'error minimizing' code hypothesis, however, including the mechanism and pathway by which an adaptive pattern of codon assignments emerged, the extent to which natural selection created synonym redundancy, its role in shaping the amino acid and nucleotide languages, and even the correct interpretation of the adaptive codon assignment pattern: these represent fertile areas for future research.

Amino Acids↗
PubMed1996

Accelerated evolution of Trimeresurus okinavensis venom gland phospholipase A2 isozyme-encoding genes.

Three Trimeresurus okinavensis (To; himehabu snake, Crotalinae) venom gland phospholipase A2 (PLA2) isozymeencoding genes, gPLA2-o1, gPLA2-o2 and gPLA2-o3, were isolated from its genomic DNA library. The nucleotide (nt) sequence analysis revealed that two of the three genes (gPLA2-o2 and gPLA2-o3) occasionally have been converted to inactivated genes by introduction of one base insertion or substitution. It was confirmed from Southern blot analysis that the To haploid genome contains only three venom gland PLA2 isozyme genes herein isolated. Comparison of these genes showed that nonsynonymous nt substitutions have occurred more frequently than synonymous nt substitutions in the protein-coding regions, except for the signal-peptide coding domain, implying that To venom gland PLA2 isozyme genes have evolved via accelerated evolution. Such an evolutionary feature of To venom gland PLA2 isozyme genes proves the general universality of accelerated evolution previously drawn for venom gland PLA2 isozyme genes of other crotalinae snakes. The variability in the mature protein-coding regions of three To venom gland PLA2 isozyme genes appears to have been brought about by natural selection for point mutations.

Amino Acid Sequence↗
PubMed1997

Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana.

To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the possibility that dimorphic DNA variation exists in the entire nuclear genome of A. thaliana. The ChiA region was divided into two blocks by an intragenic recombination between two parental sequence types, which diverged 7.4 MYA under the assumption that nucleotide mutation rate per site per year is mu = 10(-9). Nucleotide diversity in the entire ChiA region was 0.0104. Tajima's test was significantly negative for both nucleotide and indel variations, which was manifested as an excess of unique polymorphisms. However, the level and pattern of polymorphism in the ChiA region were inconsistent with simple theoretical explanations. The HKA test detected no difference in the levels of intra- and interspecific variations between the ChiA and Adh regions. In the ChiA coding region, no difference in the patterns of synonymous and replacement variation was found in intra- and interspecific comparisons by the MK test. Although it was difficult to determine the exact genetic mechanism acting on the ChA locus, these results suggested that the ChA locus region was under the same genetic mechanism before and after the establishment of A. thaliana as a species.

Alcohol Dehydrogenase↗
PubMed2006

Genetic association of the antiviral restriction factor TRIM5alpha with human immunodeficiency virus type 1 infection.

The innate antiviral factor TRIM5alpha restricts the replication of some retroviruses through its interaction with the viral capsid protein, leading to abortive infection. While overexpression of human TRIM5alpha results in modest restriction of human immunodeficiency virus type 1 (HIV-1), this inhibition is insufficient to block productive infection of human cells. We hypothesized that polymorphisms within TRIM5 may result in increased restriction of HIV-1 infection. We sequenced the TRIM5 gene (excluding exon 5) and the 4.8-kb 5' putative regulatory region in genomic DNA from 110 HIV-1-infected subjects and 96 exposed seronegative persons, along with targeted gene sequencing in a further 30 HIV-1-infected individuals. Forty-eight single nucleotide polymorphisms (SNPs), including 20 with allele frequencies of >1.0%, were identified. Among these were two synonymous and eight nonsynonymous coding polymorphisms. We observed no association between TRIM5 polymorphism in HIV-1-infected subjects and their set-point viral load after acute infection, although one TRIM5 haplotype was weakly associated with more rapid CD4(+) T-cell loss. Importantly, a TRIM5 haplotype containing the nonsynonymous SNP R136Q showed increased frequency among HIV-1-infected subjects relative to exposed seronegative persons, with an odds ratio of 5.49 (95% confidence interval = 1.83 to 16.45; P = 0.002). Nonetheless, we observed no effect of individual TRIM5alpha nonsynonymous mutations on the in vitro HIV-1 susceptibility of CD4(+) T cells. Therefore, any effect of TRIM5alpha polymorphism on HIV-1 infection in primary lymphocytes may depend on combinations of SNPs or on DNA sequences in linkage disequilibrium with the TRIM5alpha coding sequence.

Adult↗
PubMed2005

Ty1-copia group retrotransposon families in cultivated cottons G. barbadense L. identified by reverse transcriptase domain analysis.

The objective of the current study was to analyze Ty1-copia group retrotransposons in cultivated G. barbadense L. cottons. DNA sequence analysis of 27 partial reverse transcriptase sequences revealed that these elements are heterogeneous and this heterogeneity is resolved into 11 distinct families. Phylogenetic analyses provided strong bootstrap support for a monophyletic origin of plant Ty1-copia group retrotransposons, yet showed high diversity within and between Gossypium species. Furthermore, G. Barbadense element topologies are incongruent with Gossypium phylogeny. The high ratio of synonymous to nonsynonymous changes indicates that the reverse transcriptase domain of these families is evolving under purifying selection. The antiquity and wide distribution of Ty1-copia group retrotransposons illustrate their active role in shaping and evolution of the Gossypium genome.

Amino Acid Sequence↗
PubMed2003

ETOPE: Evolutionary test of predicted exons.

Since a large number of computationally predicted exons are not supported by existing sequence (e.g. ESTs) or experimental (e.g. expression analysis) data they need to be validated by other methods. ETOPE is designed to test computational predictions by using signals that have not been included in any current computational prediction method. The test is based on the ratio of non-synonymous to synonymous substitution rates between sequences from different genomes. It has been previously shown, by empirical data and computer simulation, to be a powerful criterion for identifying protein-coding regions. The ETOPE is available at http://nekrut.uchicago.edu/etope/.

Amino Acid Substitution↗
PubMed1997

Prohibitin expression is decreased in the regenerating liver but not in chemically induced hepatic tumors in rats.

Expression of prohibition, a growing-regulatory protein, was immunohistochemically investigated in normal rat tissues, regenerating livers, and chemically induced preneoplastic and neoplastic hepatic lesions. Specific cell types including hepatocytes, striated and smooth muscle cells, salivary gland duct epithelial cells, chondrocytes, immature spermatocytes and oocytes were found to be positive. In regenerating livers, prohibitin protein disappeared as early as 3 h after two-thirds hepatectomy and returned to near the original level by 24 h, while its mRNA level did not markedly vary. The timing of the disappearance was coincident with the expression of c-myc, suggesting a relation to quiescent hepatocytes entering the cell cycle. However, no pronounced decrease was evident in the most hyperplastic hepatic nodules and hepatocellular carcinomas investigated. Examination of 9 rat hepatocellular carcinoma cell lines, 6 hyperplastic hepatic nodules and 5 hepatocellular carcinomas revealed a single case of a base substitution in prohibition cDNA, identified as a synonymous sense change. The observed abundant expression of prohibitin in quiescent hepatocytes and its rapid loss under conditions of regeneration indicate a growth-regulatory function, but our results do not suggest any critical role in rat hepatocarcinogenesis.

Animals↗
PubMed2005

Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon.

DNA variation in the alcohol dehydrogenase (Adh2) region of the wild rice Oryza rufipogon and its related species was analyzed to clarify maintenance mechanisms of the DNA variation in these species. A dimorphic pattern was detected in the Adh2 region of O. rufipogon. The silent nucleotide diversity (pi) in the Adh2 region in O. rufipogon was 0.011, which was higher than that of the Adh1 region in O. rufipogon. Especially, a high nucleotide diversity was detected at synonymous sites of the catalytic domain 1. Average nucleotide diversity at silent sites within each of the dimorphic sequence types of the Adh2 region was similar to that in the Adh1 region, indicating that the high level of silent polymorphism in the Adh2 region was caused by the difference between the dimorphic sequence types. On the other hand, the level of replacement polymorphism in the Adh2 region was as low as that in the Adh1 region. The neutrality test of Fu and Li indicated significantly negative deviation from the neutral mutation model for the replacement sites of the Adh2 region. This result suggests purifying selection on the replacement sites of the Adh2 region, as detected for the Adh1 region. Significant linkage disequilibria (16.4% of the tests) were detected between the Adh1 and Adh2 regions. Even when nonrandom association was tested for the strains belonging to one of the divergent sequence types of the Adh2 region, significant interlocus linkage disequilibria were detected. The close physical distance and/or epistasis between the two Adh regions could be invoked to explain these nonrandom associations.

Alcohol Dehydrogenase↗
PubMed2006

Evolutionary simulations to detect functional lineage-specific genes.

MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.

Animals↗
PubMed1986

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

Two simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions are presented. Although they give no weights to different types of codon substitutions, these methods give essentially the same results as those obtained by Miyata and Yasunaga's and by Li et al.'s methods. Computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the number of nucleotide substitutions per site is very large. It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large.

Amino Acid Sequence↗
PubMed1996

Codon usage and base composition in Rickettsia prowazekii.

Codon usage and base composition in sequences from the A + T-rich genome of Rickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21 R. prowazekii proteins with that of a homologous set of proteins from Escherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests that R. prowazekii has around 800 genes and that 60-70% of the genome may be coding.

Base Composition↗
PubMed2004

Inhibition of lens fiber cell morphogenesis by expression of a mutant SV40 large T antigen that binds CREB-binding protein/p300 but not pRb.

Simian virus (SV) 40 large T antigen can both induce tumors and inhibit cellular differentiation. It is not clear whether these cellular changes are synonymous, sequential, or distinct responses to the protein. T antigen is known to bind to p53, to the retinoblastoma (Rb) family of tumor suppressor proteins, and to other cellular proteins such as p300 family members. To test whether SV40 large T antigen inhibits cellular differentiation in vivo in the absence of cell cycle induction, we generated transgenic mice that express in the lens a mutant version of the early region of SV40. This mutant, which we term E107KDelta, has a deletion that eliminates synthesis of small t antigen and a point mutation (E107K) that results in loss of the ability to bind to Rb family members. At embryonic day 15.5 (E15.5), the transgenic lenses show dramatic defects in lens fiber cell differentiation. The fiber cells become post-mitotic, but do not elongate properly. The cells show a dramatic reduction in expression of their beta- and gamma-crystallins. Because CBP and p300 are co-activators for crystallin gene expression, we assayed for interactions between E107KDelta and CBP/p300. Our studies demonstrate that cellular differentiation can be inhibited by SV40 large T antigen in the absence of pRb inactivation, and that interaction of large T antigen with CBP/p300 may be enhanced by a mutation that eliminates the binding to pRb.

Animals↗
PubMedDate not supplied

Episodic ataxia type 1 and 2 (familial periodic ataxia/vertigo).

Episodic ataxia (EA) is a rare, disabling condition of autosomal dominant inheritance, but it is not a distinct clinical entity. Synonyms are familial periodic ataxia or hereditary paroxysmal cerebellar ataxia. Family members have a similar clinical syndrome; however, the syndrome varies considerably from family to family. At least two groups of disorders have been separated clinically: (1) episodic ataxia type 1 (EA-1), which manifests without vertigo and is associated with 'interictal' myokymia, and (2) episodic ataxia type 2 (EA-2), which often manifests with vertigo and is associated with 'interictal' nystagmus. EA-1 and EA-2 have been identified as channelopathies. EA-1 is due to different heterozygous missense point mutations in a voltage-gated (delayed rectifier) potassium channel gene (KCNA1/Kv1.1) on chromosome 12p13, whereas EA-2 is caused by mutations of the cerebral P/Q-type calcium channel alpha 1 subunit gene CACNL1A4 localized on chromosome 19p, which is highly expressed in the cerebellum. The diagnosis of EA-1 and EA-2 is important, since they can be easily treated and are often mislabeled. As effective as acetazolamide is in preventing attacks, prospective studies still have to prove whether it can prevent progressive ataxia in EA-2 or even improve chronic cerebellar deficits.

Acetazolamide↗
PubMed2006

Phylogenetic analyses of penicillia based on partial calmodulin gene sequences.

Partial sequences (about 600 nucleotides) of the calmodulin gene were used for the phylogenetic studies on Eupenicillium, Talaromyces and Penicillium. This region is from the 3rd base of the codon for the 9th amino acid Gln to the 3rd base of the codon for the 122th amino acid Val, flanking parts of the 2nd and 5th exons with complete sequences of two exons and three introns. Seventy-six isolates of 56 taxa of penicillia were involved. The nucleotide sequences with and without introns were analyzed respectively using the neighbor-joining (NJ) and maximum parsimony (MP) methods. The cluster analysis on relative synonymous codon usage (RSCU) of each sequence was also carried out. The fact that species of penicillia belong to the two subfamilies of the Trichocomaceae proposed by Malloch based on traditional methods is supported by our molecular data, whereas, the development of asci and patterns of penicilli show little phylogenetic information. Nine groups in the lineage of Eupenicillium and two in that of Talaromyces were recognized in our studies. In addition to the teleomorph-holomorph-anamorph evolutionary model of penicillia suggested by LoBuglio et al., and Pitt, we proposed that a mutation bias of holomorphs/anamorphs with or without selection is another evolutionary path of these organisms.

Base Sequence↗
PubMed1987

Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species.

To study the rate and pattern of nucleotide substitution in mitochondrial DNA (mtDNA), we cloned and sequenced a 975-bp segment of mtDNA from Drosophila melanogaster, D. simulans, and D. mauritiana containing the genes for three transfer RNAs and parts of two protein-coding genes, ND2 and COI. Statistical analysis of synonymous substitutions revealed a predominance of transitions over transversions among the three species, a finding differing from previous results obtained from a comparison of D. melanogaster and D. yakuba. The number of transitions observed was nearly the same for each species comparison, including D. yakuba, despite the differences in divergence times. However, transversions seemed to increase steadily with increasing divergence time. By contrast, nonsynonymous substitutions in the ND2 gene showed a predominance of transversions over transitions. Most transversions were between A and T and seemed to be due to some kind of mutational bias to which the A + T-rich mtDNA of Drosophila species may be subject. The overall rate of nucleotide substitution in Drosophila mtDNA appears to be slightly faster (approximately 1.4 times) than that of the Adh gene. This contrasts with the result obtained for mammals, in which the mtDNA evolves approximately 10 times faster than single-copy nuclear DNA. We have also shown that the start codon of the COI gene is GTGA in D. simulans and GTAA in D. mauritiana. These codons are different from that of D. melanogaster (ATAA).

Amino Acid Sequence↗
PubMed2005

Sequence variation in the tRNA genes of human mitochondrial DNA.

Recent analyses have shown that nonsynonymous variation in human mitochondrial DNA (mtDNA) contains nonneutral variants, suggesting the presence of mildly deleterious mutations. Many of the disease-causing mutations in mtDNA occur in the genes encoding the tRNAs. Nucleotide sequence variation in these genes has not been studied in human populations, nor have the structural consequences of nucleotide substitutions in tRNA molecules been examined. We therefore determined the nucleotide sequences of the 22 tRNA genes in the mtDNA of 477 Finns and, also, obtained 435 European sequences from the MitoKor database. No differences in population polymorphism indices were found between the two data sets. We assessed selective constraints against various tRNA domains by comparing allele frequencies between these domains and the synonymous and nonsynonymous sites, respectively. All tRNA domains except the variable loop were more conserved than synonymous sites, and T stem and D stem were more conserved than the respective loops. We also analyzed the energetic consequences of the 96 polymorphisms recovered in the two data sets or in the Mitomap database. The minimum free energy (DeltaG) was calculated using the free energy rules as implemented in mfold version 3.1. The DeltaG's were normally distributed among the 22 wild-type tRNA genes, whereas the 96 polymorphic tRNAs departed significantly from a normal distribution. The largest differences in DeltaG between the wild-type and the polymorphic tRNAs in the Finnish population tended to be in the polymorphisms that were present at low frequencies. Allele frequency distributions and minimum free energy calculations both suggested that some polymorphisms in tRNA genes are nonneutral.

Analysis of Variance↗