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PubMed1996

Preferential RNA editing at specific sites within transcripts of two plant mitochondrial genes does not depend on transcriptional context or nuclear genotype.

Transcripts of most plant mitochondrial protein-coding genes exhibit C-to-U RNA editing events. In Petunia, two co-transcribed genes, nad3 and rps12, exhibit transcripts which are not fully edited at all potential editing sites. We investigated the nad3/rps12 transcript population in four different genotypes. In one pair of genotypes, the nuclear genome is identical but the nad3/rps12 genes are in different transcriptional contexts. Both the nad3/ rps12 genes and the plant mitochondrial genomes are identical in a second pair of genotypes, but the nuclear background is derived from two different Petunia species. We found that the overall extent of editing varied greatly between genotypes and is affected by nuclear genotype but not by the global transcriptional context. Local sequence context around a particular site does affect editing frequency. In all genotypes, certain sites exhibit high editing frequency, but these sites do not share obvious primary sequence characteristics. In all genotypes examined, editing sites which do not affect the encoded amino acid are less frequently edited than sites which alter codons to non-synonymous forms. All these data indicate that an unidentified property of the sequences immediately surrounding a cytosine affect its selection as a target in the editing process.

Amino Acid Sequence↗
PubMedDate not supplied

Isolation of major histocompatibility complex class I cDNA from pink salmon (Oncorhynchus gorbuscha).

An MHC class I cDNA clone was isolated from pink salmon (Oncorhynchus gorbuscha). Eight amino acids, which have been shown in mammals to bind main-chain atoms of peptides, are well conserved in the salmon alpha 1 and alpha 2 domains. Nine amino acids in the alpha 3 domain are classified by Williams and Barclay (Ref. 1. Ann. Rev. Immunol. 6:381-405, 1988) as signature immunoglobulin superfamily residues. The pink salmon MHC class I extracellular domains show 84.2% amino acid identity with those of Atlantic salmon (Sasa p30). polymorphism of the MHC class I alpha 1 domain was determined using PCR with genomic DNA from 12 fish. Sixteen variants were identified with most diversity concentrated in those amino acids that bind directly to peptides in mammalian class I molecules. Non-synonymous substitutions predominate over synonymous ones in the codons encoding these polymorphic residues.

Amino Acid Sequence↗
PubMed2001

Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b.

To predict the amino acid sites important for the clearance of hepatitis C virus (HCV) subtype 1b in vivo, positively selected amino acid sites were detected by analyzing the sequence data collected from the international DNA databank. The rate of nonsynonymous substitutions per nonsynonymous site was compared with that of synonymous substitutions per synonymous site for each codon site in the entire coding region. As a result, 13 out of 3010 amino acid sites were found to be positively selected. Among the 13 positively selected amino acid sites, eight were located in the structural proteins and five were in the nonstructural proteins. Moreover, eight were located in B-cell epitopes and two were in T-cell epitopes. These observations suggest that both the antibody and the cytotoxic T lymphocyte are involved in the clearance of HCV subtype 1b in vivo. These positively selected amino acid sites represent candidate vaccination targets for HCV subtype 1b.

Amino Acids↗
PubMed1999

A compact gene cluster in Drosophila: the unrelated Cs gene is compressed between duplicated amd and Ddc.

Cs, a gene with unknown function, and amd and Ddc, which encode decarboxylases, are among the most closely spaced genes in D. melanogaster. Untranslated 3' ends of the convergently transcribed genes Cs and Ddc are known to overlap by 88bp. A number of questions arise about the organization of this tightly-packed gene region and about the evolution and function of the Cs gene. We have now investigated this three-gene cluster in Scaptodrosophila lebanonensis (which diverged from D. melanogaster 60-65 MYA), as well as in D. melanogaster and D. simulans. Gene order and direction of transcription is the same in all three species. The Cs gene codes, in Scaptodrosophila, for a polypeptide of 544 amino acids; in D. melanogaster, it consists of 504 amino acids, which is twice as long as previously suggested, which makes the gene density even more spectacular. The Cs sequences exhibit higher number of non-synonymous substitutions between species, higher ratios of non-synonymous to synonymous substitutions, and lower codon usage bias than other genes, suggesting that Cs is less functionally constrained than the other genes. This is consistent with the failure of inducing phenotypic mutations in D. melanogaster. The function of Cs remains to be identified, but a high degree of similarity indicates that it is homologous to genes coding for a corticosteroid-binding protein in yeast and a polyamine oxidase in maize.

Amino Acid Sequence↗
PubMed1994

Allelic polymorphism in the coding region of human TCR C alpha gene and characterization of structural variability in the alpha chain constant domain.

An allelic variant of the human TCR C alpha gene, designated C alpha AL, which encodes a structurally different protein product has been characterized. C alpha AL was independently sequenced using polymerase chain reaction (PCR)-amplified TCR C alpha cDNA from various T cell clones derived from a same individual. It differed from the most usual C alpha sequence by two non-synonymous base changes at codons 4 (AAC-->AAG) and 84 (GAA-->GCA) of the C alpha coding region. These changes imply amino acid substitutions Asn-->Lys and Glu-->Ala respectively. An oligotyping method, based on hybridization of allele-specific oligonucleotides to PCR-amplified C alpha DNA, is also described. It was used for differential typing of the two C alpha forms in family and population studies. In each of three T cell clones analyzed from the same donor having two rearranged TCR alpha chain transcripts, C alpha AL was found in only one of the transcripts. In addition, C alpha AL segregated as a co-dominant mendelian allele within the family of this donor. Population analysis was carried out in 73 spanish individuals. Twelve donors (16.4%) were heterozygous, implying that C alpha AL was present in this population sample with an allelic frequency of 0.08. The observed frequencies of C alpha genotypes were those expected for the two alleles being in Hardy-Weinberg equilibrium. This demonstration of structural polymorphism in the constant region of TCR alpha chains provides a useful genetic marker for TCR and disease association studies due to its precise mapping within the C alpha coding region, and its significant frequency in the analyzed population.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed2004

The human serotonin receptor 2B: coding region polymorphisms and association with vulnerability to illegal drug abuse.

OBJECTIVE AND METHODS: 5-Hydroxytryptamine (serotonin) receptor 2B (HTR2B) is involved in brain development. Although expressed in the human brain, HTR2B has not been investigated much for its role in higher brain functions. Here we describe a genome-scan with 391 simple sequence repeat markers in 300 Caucasians, identifying HTR2B gene as a candidate for drug abuse vulnerability. RESULTS: From DNA re-sequencing of 110 subjects, we discovered three novel single nucleotide polymorphisms (SNPs), two of which confer a double-mutant of the receptor protein in a drug-abusing population. Arg6, a conserved basic residue, and the conserved acidic Glu42 are mutated simultaneously into Gly, termed R6G/E42G. Furthermore, this double-mutant tends to associate with drug abuse (P = 0.08 by chi2 test). The third SNP that is a synonymous mutation in the codon of Gln11 showed significant association with drug abuse (P = 0.0335 by Fisher's exact test). CONCLUSION: Our data are the first suggesting that HTR2B contributes to brain architecture and pathways that are involved in illegal drug reward.

Adult↗
PubMed2005

Description of a new HLA-DRB1*1104, DRB1*110403.

We report here the exon 2 sequence of the novel HLA-DRB1*110403 which differs from DRB1*110401 by a single synonymous nucleotide substitution at codon 78, where TAC is substituted by TAT. The variant originally identified in a Caucasoid individual was confirmed by cloning and sequencing.

Alleles↗
PubMed1998

Natural selection at major histocompatibility complex loci of vertebrates.

The loci of the vertebrate major histocompatibility complex encode cell-surface glycoproteins that present peptides to T cells. Certain of these loci are highly polymorphic, and the mechanisms responsible for this polymorphism have been intensely debated. Four independent lines of evidence support the hypothesis that MHC polymorphisms are selectively maintained: (a) The distribution of allelic frequencies does not fit the neutral expectation. (b) The rate of nonsynonymous nucleotide substitution significantly exceeds the rate of synonymous substitution in the codons encoding the peptide-binding region of the molecule. (c) Polymorphisms have been maintained for long periods of time ("trans-species polymorphism"). (d) Introns have been homogenized relative to exons over evolutionary time, suggesting that balancing selection acts to maintain diversity in the latter, in contrast to the former.

Animals↗
PubMed2026

Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.

Could codon composition condition the immediate success and the orientation of horizontal gene transfer? Horizontal gene transfer represents a change in the genome of expression of the transferred gene, and experimental evidence has accumulated indicating that the codon composition of a sequence is an important determinant of its compatibility with the translation machinery of the genome in which it is expressed. This suggests that codon composition influences the phenotype and the fitness conferred by a transferred gene and thus the immediate success of the transfer. To directly test this hypothesis, we characterized the resistance conferred by synonymous variants of a gentamicin resistance gene in three bacterial species: Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. The strongest determinant of the resistance level conferred was the species in which the resistance gene was transferred, very likely because of important differences in the copy number of the plasmid carrying the gene. Significant differences in resistance were also found between synonymous variants within each of the three species, but more importantly, there was a strong interaction between species and variant: variants conferring high resistance in one species confer low resistance in another. However, the similarity in codon usage between the synonymous variants and the host genome only explained part of the phenotypic differences between variants in one species, P. aeruginosa. Further investigation of alternative explanations did not reveal common universal mechanisms across our three bacterial species. We conclude that codon composition can be a determinant of post-horizontal gene transfer success. However, there are multiple paths leading from synonymous sequence to phenotype, and sensitivity to these different paths is species-specific.

Gene Transfer, Horizontal↗
PubMed1993

Forbidden synonymous substitutions in coding regions.

In the evolution of highly conserved genes, a few "synonymous" substitutions at third bases that would not alter the protein sequence are forbidden or very rare, presumably as a result of functional requirements of the gene or the messenger RNA. Another 10% or 20% of codons are significantly less variable by synonymous substitution than are the majority of codons. The changes that occur at the majority of third bases are subject to codon usage restrictions. These usage restrictions control sequence similarities between very distant genes. For example, 70% of third bases are identical in calmodulin genes of man and trypanosome. Third-base similarities of distant genes for conserved proteins are mathematically predicted, on the basis of the G+C composition of third bases. These observations indicate the need for reexamination of methods used to calculate synonymous substitutions.

Actins↗
PubMed1992

Context rules of rightward overlapping reading.

We have investigated the mechanism and sequence context rules governing ribosome frameshifting promoted by aminoacyl-tRNA limitation. In the case of one shifty sequence, frameshifting promoted by lysyl-tRNA limitation occurs at the sequence AAG C and is due to rightward movement of the ribosome so as to read the AGC triplet overlapping the hungry codon from the right. The frequency of this event is unaffected by sequence elements more than three bases to the left (upstream) or two bases to the right (downstream) of the hungry codon, and only slightly affected by the identity of the base two bases to the right. It is strongly affected by the base immediately to the right of the hungry codon, which becomes the wobble base of the shifted triplet; and by the third base of the hungry codon, even though the two synonyms (AAG and AAA) call for the same aminoacyl-tRNA; and by the identity of the base immediately to the left of the hungry codon. The latter result suggests that the aminoacyl-tRNA in the P site affects the maintenance of reading frame at the adjacent A site of the ribosome. However, the DNA sequence makes it seem unlikely that the P-site tRNA shifts to the right in concert with the A-site tRNA, a mechanism that can account for leftward frameshifting (in the opposite direction) in retroviral translation. The specificity of sequence determinants of leftwing versus rightwing frameshifting is discussed.

Amino Acid Sequence↗
PubMed1993

Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome.

The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be influenced by the compartmentalization of their genomes into fractions of distinct base composition and mutational properties. We have examined the Drosophila genome to explore relationships between the nucleotide content of large chromosomal segments and the base composition and rate of evolution of genes within those segments. Direct determination of the G + C contents of yeast artificial chromosome clones containing inserts of Drosophila melanogaster DNA ranging from 140-340 kb revealed significant heterogeneity in base composition. The G + C content of the large segments studied ranged from 36.9% G + C for a clone containing the hunchback locus in polytene region 85, to 50.9% G + C for a clone that includes the rosy region in polytene region 87. Unlike other organisms, however, there was no significant correlation between the base composition of large chromosomal regions and the base composition at fourfold degenerate nucleotide sites of genes encompassed within those regions. Despite the situation seen in mammals, there was also no significant association between base composition and rate of nucleotide substitution. These results suggest that nucleotide sequence evolution in Drosophila differs from that of many vertebrates and does not reflect distinct mutational biases, as a function of base composition, in different genomic regions. Significant negative correlations between codon-usage bias and rates of synonymous site divergence, however, provide strong support for an argument that selection among alternative codons may be a major contributor to variability in evolutionary rates within Drosophila genomes.

Animals↗
PubMed2004

On the role of the starved codon and the takeoff site in ribosome bypassing in Escherichia coli.

Translating ribosomes can skip over stretches of messenger RNA and resume protein chain elongation after a "bypassed" region. We have previously shown that limitation for isoleucyl-tRNA can initiate a ribosome bypass when an AUA codon is in the ribosomal A-site. We have now generalized this effect to other "hungry" codons calling for four different limiting aminoacyl-tRNA species, suggesting that a pause at any A-site will have this effect. We have assessed bypassing in a large family of reporters with nearly every different triplet in the "takeoff site", i.e. the P-site on the 5' side of the hungry codon, and an identical "landing site" codon 16 nucleotides downstream. The different takeoff sites vary over a factor of 50 in bypassing proficiency. At least part of this variation appears to reflect stability of the codon Colon, two colons anticodon interaction at the takeoff site, as indicated by the following: (a) the bypassing proficiency of different tRNAs shows a rough correlation with the frequency of A Colon, two colons U as opposed to G Colon, two colons C pairs in the codon Colon, two colons anticodon association; (b) specific tRNAs bypass more frequently from codons ending in U than from their synonym ending in C; (c) an arginine tRNA with Inosine in the wobble position which reads CGU, CGC, and CGA bypasses much more frequently from the last codon than the first two synonyms.

Amino Acid Sequence↗
PubMed2001

ADAPTSITE: detecting natural selection at single amino acid sites.

UNLABELLED: ADAPTSITE is a program package for detecting natural selection at single amino acid sites, using a multiple alignment of protein-coding sequences for a given phylogenetic tree. The program infers ancestral codons at all interior nodes, and computes the total numbers of synonymous (c(S)) and nonsynonymous (c(N)) substitutions as well as the average numbers of synonymous (s(S)) and nonsynonymous (s(N)) sites for each codon site. The probabilities of occurrence of synonymous and nonsynonymous substitutions are approximated by s(S) / (s(S) + s(N)) and s(N) / (s(S) + s(N)), respectively. The null hypothesis of selective neutrality is tested for each codon site, assuming a binomial distribution for the probability of obtaining c(S) and c(N). AVAILABILITY: ADAPTSITE is available free of charge at the World-Wide Web sites http://mep.bio.psu.edu/adaptivevol.html and http://www.cib.nig.ac.jp/dda/yossuzuk/welcome.html. The package includes the source code written in C, binary files for UNIX operating systems, manual, and example files.

Algorithms↗
PubMed1999

Symmetry breaking and adaptation: evidence from a 'toy model' of a virus.

We argue that an induced breaking of the genetic synonym symmetry due to the action of genetic operators such as mutation can enhance the adaptability of a species to changes in the environment. In the case of a virus, the claim is that the codon bias in the neutralization epitope improves the virus' ability to generate mutants that evade the induced immune response. We support our claim with a simple 'toy model' of a viral epitope evolving in competition with the immune system. The effective selective advantage of a higher mutability leads to a dominance of codons that favor non-synonymous mutations. As further evidence we present a simple model for a genetic regulatory network that leads to adaptive evolution in a population of giraffes by means of an induced symmetry breaking rather than through any direct selective advantage.

Adaptation, Physiological↗
PubMed2004

Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii, (2) the fungi Saccharomyces cerevisiae and S. paradoxus, and (3) the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected, given the nature of the genetic code.

Animals↗
PubMed2004

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.

Sequencing of multiple, nearly complete eukaryotic genomes creates opportunities for detecting previously unnoticed, subtle functional signals in non-coding regions. A genome-wide comparative analysis of orthologous sets of mammalian and yeast mRNAs revealed distinct patterns of evolutionary conservation at the boundaries of the untranslated regions (UTRs) and the coding region (CDS). Elevated sequence conservation was detected in approximately 30 nt regions around the start codon. There seems to be a complementary relationship between sequence conservation in the approximately 30 nt regions of the 5'-UTR immediately upstream of the start codon and that in the synonymous positions of the 5'-terminal 30 nt of the CDS: in mammalian mRNAs, the 5'-UTR shows a greater conservation than the CDS, whereas the opposite trend holds for yeast mRNAs. Unexpectedly, a approximately 30 nt region downstream of the stop codon shows a substantially lower level of sequence conservation than the downstream portions of the 3'-UTRs. However, the sequence in this poorly conserved 30 nt portion of the 3'-UTR is non-random in that it has a higher GC content than the rest of the UTR. It is hypothesized that the elevated sequence conservation in the region immediately upstream of the start codon is related to the requirement for initiation factor binding during pre-initiation ribosomal scanning. In contrast, the poorly conserved region downstream of the stop codon could be involved in the post- termination scanning and dissociation of the ribosomes from the mRNA, which requires only the mRNA-ribosome interaction. Additionally, it was found that the choice of the stop codon in mammals, but not in yeasts, and the context in the immediate vicinity of the stop codons in both mammals and yeasts are subject to strong selection. Thus, genome-wide analysis of orthologous gene sets allows detection of previously unrecognized patterns of sequence conservation, which are likely to reflect hidden functional signals, such as ribosomal filters that could regulate translation by modulating the interaction between the mRNA and ribosomes.

3' Untranslated Regions↗