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PubMed2005

Empirical codon substitution matrix.

BACKGROUND: Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. RESULTS: A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 x 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 x 61 entries for the sense codons and 3 x 3 entries for the stop codons. CONCLUSION: The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.

Amino Acid Substitution↗
PubMed2006

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa.

BACKGROUND: The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine, citrus and many other plant species. Despite its economic impact, relatively little is known about the genomic variations among strains isolated from different hosts and their influence on the population genetics of this pathogen. With the availability of genome sequence information for four strains, it is now possible to perform genome-wide analyses to identify and categorize such DNA variations and to understand their influence on strain functional divergence. RESULTS: There are 1,579 genes and 194 non-coding homologous sequences present in the genomes of all four strains, representing a 76. 2% conservation of the sequenced genome. About 60% of the X. fastidiosa unique sequences exist as tandem gene clusters of 6 or more genes. Multiple alignments identified 12,754 SNPs and 14,449 INDELs in the 1528 common genes and 20,779 SNPs and 10,075 INDELs in the 194 non-coding sequences. The average SNP frequency was 1.08 x 10(-2) per base pair of DNA and the average INDEL frequency was 2.06 x 10(-2) per base pair of DNA. On an average, 60.33% of the SNPs were synonymous type while 39.67% were non-synonymous type. The mutation frequency, primarily in the form of external INDELs was the main type of sequence variation. The relative similarity between the strains was discussed according to the INDEL and SNP differences. The number of genes unique to each strain were 60 (9a5c), 54 (Dixon), 83 (Ann1) and 9 (Temecula-1). A sub-set of the strain specific genes showed significant differences in terms of their codon usage and GC composition from the native genes suggesting their xenologous origin. Tandem repeat analysis of the genomic sequences of the four strains identified associations of repeat sequences with hypothetical and phage related functions. CONCLUSION: INDELs and strain specific genes have been identified as the main source of variations among strains, with individual strains showing different rates of genome evolution. Based on these genome comparisons, it appears that the Pierce's disease strain Temecula-1 genome represents the ancestral genome of the X. fastidiosa. Results of this analysis are publicly available in the form of a web database.

Analysis of Variance↗
PubMed2002

Molecular tumour clocks and colorectal cancer: seeing the unseen.

Recent advances in mathematics and sequencing have revolutionised the analysis of evolution. Modern phylogeny is molecular phylogeny, or histories reconstructed from sequences. The same quantitative sequence approaches have not been fully translated to colorectal cancer. Molecular tumour clocks provide opportunities to reconstruct individual tumour histories. Phenotypic and genetic progression are usually thought to be synonymous, but many mutations may accumulate in normal appearing cells. Although such occult genetic progression is essentially invisible, molecular tumour clocks offer the somewhat magical ability to reconstruct what may never be seen. Potentially much of colorectal cancer progression is unseen and unexplored because tumours usually appear late in life.

Animals↗
PubMed2006

[Effects of MTNR1A gene on litter size in a large white and a landrace herd].

Two pairs of primers were designed based on the known sequence in GenBank for amplification of MTNR1A gene in a Large White and a Landrace herd. Using PCR-SSCP (single strand conformation polymorphism), we found a single nucleotide polymorphism(SNP) within the product amplified from the first pair of primers. PCR products from randomly selected different genotypes were sequenced after were recovered and purified. Results revealed a synonymous single base mutation(G-->A) at +159bp(sequence numbering based on Genbank accession number U73326) for the BB genotype. When analyzed for association with litter size traits, this MTNR1A SNP was found to have no significant effect on litter size traits.

Animals↗
PubMed2006

Genetic diversity of Plasmodium vivax Pvcsp and Pvmsp1 in Guyana, South America.

Approximately 55% of malaria infections in the Guyana Amazon region are attributed to Plasmodium falciparum while the other 45% are attributed to non-falciparum, mostly Plasmodium vivax. However, little is known about the P. vivax strain types circulating in the region. Using PCR for Plasmodium detection and two genetic markers specific to P. vivax to detect the polymorphic circumsporozoite protein (CSP) and the conserved 19-kDa region of the merozoite surface protein-1 (MSP-1), we investigated the overall Plasmodium strain distribution and population diversity within P. vivax in isolates collected from the blood of infected individuals in the interior Amazon region of Guyana, South America. Out of a total of 250 samples positive for Plasmodium, P. vivax was detected in 30% (76/250) and P. falciparum was detected in 76% (189/250). Mixed infections containing both P. falciparum and P. vivax constituted 6% (15/250) of the total positive samples. Further analysis of P. vivax strains showed that 92% (56/61) of the P. vivax samples hybridized with a probe specific to type VK210, 39% (24/61) hybridized with a probe specific for type VK247, and 25% (15/61) hybridized with a probe specific for the P. vivax-like CS genotype. DNA sequencing of the 19-kDa C-terminal domain in block 13 of MSP-1 amplified from 61 samples from patients infected with P. vivax demonstrated that this region is highly conserved, and all samples were identical at the nucleotide level to the Belem and Salvador-1 types. No synonymous or nonsynonymous mutations were observed in this region of the gene, indicating that current vaccine-development efforts based on the MSP-1(19) fragment would be applicable in Guyana.

Animals↗
PubMedDate not supplied

Immunohistochemical detection of p53 protein in HPV positive oral lesions.

Oral cancer provides a unique model system for the study of the multistep nature of cancer. The influence of viruses and tumor suppressor gene inactivation are of major importance in this HPVs are small oncogenic viruses which are implicated in epithelial carcinogenesis, and p53 is a tumor suppressor gene with a central role in the prevention of genomic injury. p53 protein detection is usually a synonym for p53 mutation. This study was designed to determine the immunohistochemical detection of p53 protein in HPV positive oral squamous cell carcinomas and hyperplastic oral lesions. p53 was detected in 50% (5/10) of HPV positive hyperplastic oral lesions and in 59.41% (22/39) of oral squamous cell carcinomas. These results indicate that HPV and p53 protein alterations frequently coexist in the lesions of our study and suggest that p53 mutation may be an early genetic event in oral carcinogenesis. Moreover, this coexistance reveals that other environmental carcinogens have a more prominent role in oral carcinogenesis, one that overrides the action of HPV.

Carcinoma, Squamous Cell↗
PubMed1998

Methods for the detection of non-random base substitution in virus genes: models of synonymous nucleotide substitution in picornavirus genes.

A substantial fraction of phylogenetic divergence between closely related RNA virus genes is generally accounted for by synonymous (non-amino acid changing) point mutation. Viral evolution may be a complicated phenomena, governed by many different processes. However in this study we ask whether there are any properties in the patterns of synonymous nucleotide substitutions in three different Picornavirus genes that permit the process of accumulation of synonymous point mutation in these genes to be distinguished from some of the simplest most basic evolutionary models. We conclude that while the observed patterns in the occurrence of synonymous point substitution are consistent with those predicted by a model in which base mutation is equi-probable along a gene, and the probability of synonymous substitution determined only by local codon usage, some patterns in the actual nucleotides exchanged remain to be explained.

Amino Acid Substitution↗
PubMed2003

The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias.

Most methods for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be synonymous under the model of evolution being considered. Here we demonstrate that this definition of a site can give misleading results and that a physical definition of site should be used in some circumstances. We illustrate our point by reexamining the relationship between codon usage bias and the synonymous substitution rate. It has recently been shown that the rate of synonymous substitution, calculated using the Goldman-Yang method, which encapsulates the mutational-opportunity definition of a site at a high level of sophistication, is either positively correlated or uncorrelated to synonymous codon bias in Drosophila. Using other methods, which account for synonymous codon bias but define a site physically, we show that there is a negative correlation between the synonymous substitution rate and codon bias and that the lack of a negative correlation using the Goldman-Yang method is due to the way in which the number of synonymous sites is counted. We also show that there is a positive correlation between the synonymous substitution rate and third position GC content in mammals, but that the relationship is considerably weaker than that obtained using the Goldman-Yang method. We argue that the Goldman-Yang method is misleading in this context and conclude that methods that rely on a mutational-opportunity definition of a site should be used with caution.

Animals↗
PubMed2003

Sex-linked mammalian sperm proteins evolve faster than autosomal ones.

X-linked genes can evolve slower or faster depending on whether most recessive, or at least partially recessive alleles are deleterious or beneficial due to their hemizygous expression in males. Molecular studies of X chromosome divergence have provided conflicting evidence for both a higher and lower rate of nucleotide substitution at both synonymous and nonsynonymous sites, depending on the nucleotide sites sampled. Using human and mouse orthologous genes, we tested the hypothesis that genes encoding male-specific sperm proteins are evolving faster on the X chromosome compared with autosomes. X-linked sperm proteins have an average nonsynonymous mutation rate almost twice as high as sperm genes found on autosomes, unlike other tissue-specific genes, where no significant difference in the nonsynonymous mutation rate between the X chromosome and autosomes was found. However, no difference was found in the average synonymous mutation rate of X-linked versus autosomal sperm proteins, which along with corresponding higher values of Ka/Ks in X-linked sperm proteins suggest that differences in selective forces and not mutation rates are the underlying cause of higher X-linked mammalian sperm protein divergence.

Animals↗
PubMed1990

Switches in species-specific codon preferences: the influence of mutation biases.

A model of synonymous codon usage is developed in which the most frequent codons are selectively advantageous because of their coadaptation with tRNA abundances. Random drift opposes the progress of this coevolution by pushing codon frequencies in the direction of the frequency that would result from mutation in the absence of selection. It is predicted that, within a certain range, an increased mutation bias away from an advantageous codon has little influence on its usage in highly expressed genes. However, a subsequent small increase in mutation bias over a critical range leads to a large reduction in the frequency of the codon. The switch in preference from one synonym to another is a sharp transition, with no stable intermediate state in which neither codon is advantageous. Codon usage patterns were compared among three related bacterial species of differing genomic G & C contents, Escherichia coli, Serratia marcescens, and Proteus vulgaris. It was found that although changes in mutation biases do not always result in switches in codon preferences, some switches have occurred in the direction of species-specific mutation biases. Fluctuating mutation biases may therefore be the main cause of differences between species in their codon preferences.

Amino Acids↗
PubMed2004

Selection on codon usage in Drosophila americana.

Synonymous codons are not used at random, significantly influencing the base composition of the genome. The selection-mutation-drift model proposes that this bias reflects natural selection in favor of a subset of preferred codons. Previous estimates in Drosophila of the intensity of selective forces involved seem too large to be reconciled with theoretical predictions of the level of codon bias. This probably results from confounding effects of the demographic histories of the species concerned. We have studied three species of the virilis group of Drosophila, which are more likely to satisfy the assumptions of the evolutionary models. We analyzed the patterns of polymorphism and divergence in a sample of 18 genes and applied a new method for estimating the intensity of selection on synonymous mutations based on the frequencies of unpreferred mutations among polymorphic sites. This yielded estimates of selection intensities (N(e)s) of the order of 0.65, which is more compatible with the observed levels of codon bias. Our results support the action of both selection and mutational bias on codon usage bias and suggest that codon usage and genome base composition in the D. americana lineage are in approximate equilibrium. Biased gene conversion may also contribute to the observed patterns.

Animals↗
PubMed2003

Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes.

Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%-60% higher mutation rate in exons than in noncoding DNA. We propose a differential CpG content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. We find that the increased exonic rate is the result of the relative overabundance of synonymous sites involved in CpG dinucleotides, as the evolutionary divergence in non-CpG sites is similar in noncoding DNA and synonymous sites of exons. Expectations and predictions of our hypothesis are confirmed in comparisons involving more distantly related species, including human-orangutan, human-baboon, and human-macaque. Our results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms (SNPs) in the synonymous sites of exons compared to the noncoding regions.

Animals↗
PubMed2000

Fluctuating mutation bias and the evolution of base composition in Drosophila.

The idea that the pattern of point mutation in Drosophila has remained constant during the evolution of the genus has recently been challenged. A study of the nucleotide composition focused on the Drosophila saltans group has evidenced unsuspected nucleotide composition differences among lineages. Compositional differences are associated with an accelerated rate of amino acid replacement in functionally less constrained regions. Here we reassess this issue from a different perspective. Adopting a maximum-likelihood estimation approach, we focus on the different predictions that mutation and selection make about the nonsynonymous-to-synonymous rate ratio. We investigate two gene regions, alcohol dehydrogenase (Adh) and xanthine dehydrogenase (Xdh), using a balanced data set that comprises representatives from the melangaster, obscura, saltans, and willistoni groups. We also consider representatives of the Hawaiian picture-winged group. These Hawaiian species are known to have experienced repeated bottlenecks and are included as a reference for comparison. Our results confirm patterns previously detected. The branch ancestral to the fast-evolving willistoni/saltans lineage, where most of the change in GC content has occurred, exhibits an excess of synonymous substitutions. The shift in mutation bias has affected the extent of the rate variation among sites in Xdh.

Alcohol Dehydrogenase↗
PubMed1994

Dimorphism and intergenic recombination within the microneme protein (MP-1) gene family of Plasmodium knowlesi.

The microneme protein-1 (MP-1) of Plasmodium knowlesi and Plasmodium vivax facilitates merozoite invasion of the erythrocyte by binding to Duffy blood group antigens. Since this protein is important in the invasion process and is a potential vaccine candidate, it is important to understand the nature of diversity within the MP-1 gene. Nine MP-1 gene sequences were compared from 2 isolates of P. knowlesi and a laboratory strain of P. vivax. The MP-1 genes of P. knowlesi were dimorphic based upon the central hydrophilic regions (III and IV) that were well conserved as alpha and beta types. Other regions were conserved among all P. knowlesi genes except for the amino cysteine-rich region (region II), a region predicted to be the initial contact site of the erythrocyte binding domain. Two distinct sequence motifs and part of a third were identified in region II that had a common identity of 68%. In some MP-1 genes recombination had occurred to create hybrids of the two sequence types. All cysteines and aromatic amino acids of region II were conserved in all genes or within a sequence type. There were 2 apparent recombination points within region II where switching occurred between sequence types. Another possible recombination site, identified as a common sequence motif, was identified in the middle of the hydrophilic region, at the beginning of regions III or IV. Nonsynonymous mutations within region II were biased towards radical amino acid changes, especially towards the carboxyl third, where there were 3 distinct types of sequence. Most synonymous and nonsynonymous nucleotide mutations within regions I, V, and VI were infrequent, individual events and not associated with any particular sequence type. Cysteine-rich regions of the P. vivax MP-1 gene compared to the P. knowlesi genes were characterized by an increased number of synonymous and nonsynonymous changes. This data identifies 2 mechanisms for generation of diversity in the MP-1 gene family, intergenic recombination and nucleotide mutations. Both may be mechanisms the parasite uses to evade the host immune response or to alter erythrocyte receptor specificity.

Amino Acid Sequence↗
PubMed1997

Codon bias evolution in Drosophila. Population genetics of mutation-selection drift.

Although non-random patterns of synonymous codon usage are a prominent feature in the genomes of many organisms, the relatives roles of mutational biases and natural selection in maintaining codon bias remain a contentious issue. In some species, patterns of codon bias and empirical findings on the biology of translation suggest 'major codon preference', a balance among mutation pressure, genetic drift, and weak selection in favor of translationally superior codons. Population genetics theory makes testable predictions to distinguish such a model from a strictly mutational model of codon bias. Major codon preference predicts two fitness classes of synonymous DNA changes: 'preferred' mutations from non-major to major codons and 'unpreferred' changes in the opposite direction. An extension of current statistical methods is employed to reveal differences in the within and between species dynamics of preferred and unpreferred silent mutations in Drosophila simulans. In this lineage, codon bias appears to be maintained under roughly equal magnitudes of natural selection and genetic drift. In the sibling species, D. melanogaster, however, a reduction in N(e)s, the product of effective population size and selection coefficient, appears to have allowed a genome-wide reduction in codon bias.

Animals↗
PubMed2004

Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.

Animals↗
PubMed1994

Characterization of a cystathionine beta-synthase allele with three mutations in cis in a patient with B6 nonresponsive homocystinuria.

We used SSCP to survey reverse transcribed-PCR amplified cystathionine synthase cDNAs from patients with homocystinuria. In a single CBS allele, we identified one synonymous and two missense mutations in a portion of the cDNA encoded by a single 135 bp exon which also encodes K119, the putative site of cofactor, pyridoxal 5'-phosphate, binding. The patient, a B6-nonresponsive homocystinuric of Irish descent, is homozygous for a G-->A transition at cDNA position 374, a G-->A transversion at position 393, and a G-->A transition at position 453 resulting in R125Q, E131D and P145P, respectively. Family studies confirmed that all three mutations are present in cis and none were present in 54 Irish and 58 North American controls. R125 is conserved in rat CBS while E131D is conserved in rat CBS, and a related enzyme, O-acetylserine(thiol)-lyase, from a variety of plant and bacterial species. Expression studies showed that both R125Q and E131D, either individually or together, inactivate CBS. The apparently simultaneous appearance of more than one mutation in a single exon suggests they may have arisen by a gene conversion event or by nonhomologous recombination.

Alleles↗
PubMed2004

Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence.

We report the results of a comprehensive study of the influence of gene expression on synonymous codons, amino acid composition, and intron presence and size in human protein-coding genes. First, in addition to a strong effect of isochores, we have detected the influence of transcription-associated mutational biases (TAMB) on gene composition. Genes expressed in different tissues show diverse degrees of TAMB, with genes expressed in testis showing the greatest influence. Second, the study of tissues with no evidence of TAMB reveals a consistent set of optimal synonymous codons favored in highly expressed genes. This result exposes the consequences of natural selection on synonymous composition to increase efficiency of translation in the human lineage. Third, overall amino acid composition of proteins closely resembles tRNA abundance but there is no difference in amino acid composition in differentially expressed genes. Fourth, there is a negative relationship between expression and CDS length. Significantly, this is observed only among genes with introns, suggesting that the cause for this relationship in humans cannot be associated only with costs of amino acid biosynthesis. Fifth, we show that broadly and highly expressed genes have more, although shorter, introns. The selective advantage for having more introns in highly expressed genes is likely counterbalanced by containment of transcriptional costs and a minimum exon size for proper splicing.

Amino Acids↗