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1.
On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses 总被引:1,自引:0,他引:1
Angelo Pavesi Bettina De Iaco Maria Ilde Granero Alfredo Porati 《Journal of molecular evolution》1997,44(6):625-631
In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region
of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging
to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap
a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the
nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and
plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both
types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation
between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses,
indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage
correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison
of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine,
leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed
as a way with which they may expand their coding ability and gain new, specialized functions.
Received: 28 October 1996 / Accepted: 29 January 1997 相似文献
2.
Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances
sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization
protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5′ end of the sperm
bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of
the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates
moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible
to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide
substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald
and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms
observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting
that the polymorphism observed in the 5′ region of S. franciscanus bindin is a result of neutral evolution.
Received: 19 June 1998 / Accepted: 2 August 2000 相似文献
3.
Zelus D Robinson-Rechavi M Delacre M Auriault C Laudet V 《Journal of molecular evolution》2000,51(3):234-244
Interleukin-2 (IL-2) is a cytokine involved in induction and regulation of the immune response in mammals. There have been
numerous reports about the search for IL-2 in species other than mammals, and recently an IL-2-like gene has been isolated
in chicken. Using PCR, we searched for IL-2 gene sequences in a wide variety of mammals, including marsupials and monotremes,
as well as in birds. Although we can readily amplify IL-2 gene fragments in placental mammals, no amplification was obtained
in other species. This is best explained by very high substitution rates. This suggest that strategies to isolate IL-2 homologous
genes outside mammals should involve functional assays, as for the chicken gene, and not hybridization-based techniques. Nonsynonymous
substitution rates are especially high in ruminants, due to positive selection acting on regions important in term of structure-function.
We suggest that, although globally similar, the immune response of various mammals is not identical, mainly at the level of
cytokine-mediated regulations.
Received: 27 July 1999 / Accepted: 15 April 2000 相似文献
4.
Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages 总被引:8,自引:0,他引:8
Brian R. Morton 《Journal of molecular evolution》1998,46(4):449-459
In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study
the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each
gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons
based on the nucleotide composition of noncoding regions of that genome. The codon bias of the actual gene is then compared
to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias
is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among
the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation
efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities
in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity
among the various genomes are discussed.
Received: 6 June 1997 / Accepted: 24 July 1997 相似文献
5.
Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection 总被引:7,自引:0,他引:7
Héctor Musto Héctor Romero Alejandro Zavala Kamel Jabbari Giorgio Bernardi 《Journal of molecular evolution》1999,49(1):27-35
We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly
biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among
genes. At one end genes display codon choices determined mainly by the extreme genome composition of this parasite, and very
probably their expression level is low. At the other end a few genes exhibit an increased relative usage of a particular subset
of codons, many of which are C-ending. Since the majority of these few genes is putatively highly expressed, we postulate
that the increased C-ending codons are translationally optimal. In conclusion, while codon usage of the majority of P. falciparum genes is determined mainly by compositional constraints, a small number of genes exhibit translational selection.
Received: 10 November 1998 / Accepted: 28 January 1999 相似文献
6.
Fimbriae or pili are essential adherence factors usually found in pathogenic bacteria to aid colonization of host cells.
Three major structural pilin genes, fimA, sfaA, and papA, from Escherichia coli natural isolates were examined and nucleotide sequence data revealed elevated levels of both synonymous and nonsynonymous
site variation at these loci. Examination of synonymous site variation shows a fivefold increase in fimA sites, relative to the housekeeping gene mdh; and similarly the sfaA and papA genes have increased synonymous sites variation relative to fimA. Nonsynonymous site variation is also elevated at all three loci but, in particular, at the papA locus (k
N= 0.44). The k
N/k
S ratio for the three genes are among the highest yet reported for E. coli genes. Regional variation in nucleotide polymorphism within each of the genes reveal hypervariable segments where nonsynonymous
substitutions exceed synonymous substitutions. We propose that at the fimA, papA, and sfaA genes, diversifying selection has brought about the increase levels of polymorphism.
Received: 7 August 1997 / Accepted: 8 March 1998 相似文献