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At least 1,225 records · Page 68Linked to original sources
PubMed1994

Molecular evolution of a Y-chromosomal repetitive sequence family in the genus Mus.

A 522-base-long Y-chromosomal sequence was isolated from a BALB/c genomic library and was designated "BF046." It is repeated about 200 times in the male genome, and a difference was detected between the Mus musculus musculus and the M. m. domesticus type Y chromosomes. BF046-related sequences were present over the entire length of the Y chromosome as visualized by in situ hybridization. Southern blot analysis against DNAs isolated from eight species in the genus Mus showed that BF046-related sequences were amplified in the Y chromosomes of three closely related species: M. musculus, M. spicilegus, and M. spretus. To gain insight into the stability of the BF046 sequence family, we isolated 18 additional clones from these three mouse species and compared their sequences. The M. musculus sequences differed from the M. spicilegus and M. spretus sequences by two indels. The remaining parts of the sequences were very similar, but both parsimony and distance-based analytical methods divided the sequences into the same four subgroups, with each species having its own subgroup(s). Thus, the Y chromosomes of M. musculus, M. spicilegus, and M. spretus can be distinguished from one another.

Animals↗
PubMed2006

Prediction of function divergence in protein families using the substitution rate variation parameter alpha.

Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with, for example, distinct substrate specificities. Detection of functionally divergent subfamilies is possible by methods for recognizing branches of adaptive evolution in a gene tree. As the number of genome sequences is growing rapidly, it is highly desirable to automatically detect subfamily function divergence. To this end, we here introduce a method for large-scale prediction of function divergence within protein families. It is called the alpha shift measure (ASM) as it is based on detecting a shift in the shape parameter (alpha [alpha]) of the substitution rate gamma distribution. Four different methods for estimating alpha were investigated. We benchmarked the accuracy of ASM using function annotation from Enzyme Commission numbers within Pfam protein families divided into subfamilies by the automatic tree-based method BETE. In a test using 563 subfamily pairs in 162 families, ASM outperformed functional site-based methods using rate or conservation shifting (rate shift measure [RSM] and conservation shift measure [CSM]). The best results were obtained using the "GZ-Gamma" method for estimating alpha. By combining ASM with RSM and CSM using linear discriminant analysis, the prediction accuracy was further improved.

Algorithms↗
PubMed1993

[Sequences resembling fragments of mitochondrial DNA in the human genome: features of evolution].

Mitochondrial-like sequences and their homologues from primate mitochondria are investigated to define direction and rate of evolution, time of integration into nuclear genome. The analysis showed that mito-like sequences differ from mitochondrial homologues by high level of symmetria of two chains of DNA. Besides that, difference between mito-like and Homo sapiens sequences in their GC-contents is found. Apparently there is GC-pressure of nuclear genome region, being the place of integration of mito-like sequence, that brings about equalization of GC-contents in nuclear region and mito-like sequences. Properties of descent mitochondrial sequence play important role in the difference of mito-like and Homo sapiens sequences also.

Base Composition↗
PubMed1992

Animal histo-blood group ABO genes.

Sequences homologous to the human histo-blood group ABO genes are present in the genomic DNA of various mammals. We have PCR-amplified, subcloned, and sequenced a portion of these genes from several species of primates and found high conservation of the nucleotide as well as the deduced amino acid sequences during evolution.

ABO Blood-Group System↗
PubMed1983

Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: its significance in gene evolution.

The complete nucleotide sequences of the 5.8S and 26S rRNA genes of Physarum polycephalum and the transcribed spacer between them were determined. Comparison of the sequences with those of the Escherichia coli 23S rRNA and yeast 26S rRNA genes showed that there are 16 highly homologous regions in the sequences of Physarum and E. coli and that eukaryotes have some eukaryote-specific extra sequences. The sequence immediately following the 5.8S-like region of E. coli 23S rRNA was found to be highly homologous to the 5' terminus of Physarum 26S rRNA, indicating that the eukaryote-specific 5.8S rRNA gene is derived from the 5'-terminal region of the prokaryote large rRNA gene.

Base Sequence↗
PubMed1996

[Calculation of specific evolution rate of proteins based on phylogenetic].

A method of calculating specific protein evolution distance and evolution rate is presented. This is based on the reconstruction of the phylogenetic tree and on the deduction of ancestral sequences according to temporally homologous protein sequences. The evolution distance and evolution rate are calculated from the difference percentage of the sequence between the temporal and deduced ancestral sequences. A comparison with Dayoff simulation method and an example of using it to calculate the specific evolution rates of mammalian erythropoietin. The method presented here would be specially useful under certain circumstances.

Amino Acid Sequence↗
PubMed1985

Concerted evolution of tRNA genes: intergenic conversion among three unlinked serine tRNA genes in S. pombe.

In many cases the multiple genes coding for one specific tRNA are dispersed throughout the genome. The members of such a gene family nevertheless maintain a common nucleotide sequence during evolution. A major mechanism contributing to this concerted evolution is intergenic conversion. Here we show that it occurs between three tRNA genes of related sequence residing on different chromosomes of Schizosaccharomyces pombe. Sequence analysis of converted genes indicates that blocks of a minimal length of 18-33 bp and of a maximal length of 190 bp can be transferred from one gene to the other. During meiosis the frequency of these transfers lies in the order of 10(-5) per progeny spore. Information transfer between any two members of the gene family occurs in both directions.

Anticodon↗
PubMed1995

Cell-cycle regulation of human B-myb transcription.

We demonstrate here that activity of the human B-myb promoter is regulated during the cell cycle by the E2 transcription factor (E2F). Comparison of the human B-myb promoter sequence with that of its murine counterpart revealed an evolutionally conserved sequence that contains an E2F-binding site. In transiently transfected murine NIH3T3 and human HaCaT cells, luciferase (Luc) reporter activity directed by the human B-myb promoter was found to increase significantly in late G1/S phase of the cell cycle. Mutation of the promoter E2F site resulted in significantly greater Luc activity in NIH3T3 and HaCaT cells made quiescent by serum deprivation, indicating that E2F repressed transcription of this gene during G0. Analysis of E2F DNA-binding activity in G0 HaCaT cells revealed a distinct complex that apparently contained neither the retinoblastoma gene protein, pRb, nor the related p107 protein. De-repression of transcription in S phase was accompanied by the disappearance of this G0 E2F complex and the appearance of a distinct complex containing p107. In addition, complexes containing pRb were detected at both stages of the cell cycle.

3T3 Cells↗
PubMed2001

Gene elements that affect the longevity of rbcL sequence-containing transcripts in Chlamydomonas reinhardtii chloroplasts.

The chloroplast gene rbcL encodes the large subunit of the CO(2)-fixing enzyme ribulose-bisphosphate carboxylase. In previous work a target for photo-accelerated degradation of Chlamydomonas reinhardtii rbcL transcripts in vivo was found to lie within the first 63 nucleotides, and a sequence element required for increasing the longevity of transcripts of rbcL-reporter genes was found to occur between nucleotides 170 and 350. Photo-accelerated degradation of rbcL transcripts has been found to require nucleotides 21 to 41. Transcript nucleotides lying between 329 and 334 and between 14 and 27 are essential for stabilizing transcripts in vivo; mutations in either region reduce the longevity of transcripts. It is postulated that the effectiveness of photo-accelerated endonuclease attacks on the nucleotide 21 to 41 region is reduced by physical blockage or distortion of the target sequence by interacting proteins that associate with nucleotides in the 14 to 27 and 329 to 334 regions of the transcripts. Both the nucleotide +329 to +334 stabilizing sequence of rbcL and a transcription enhancing sequence that lies between +126 and +170 encode well conserved (cyanobacteria through angiosperms) amino acid sequences; the evolution of expression control elements within the protein coding sequence of rbcL is considered.

Animals↗
PubMed1996

Genome rearrangements of rotaviruses.

Rotaviruses (and other members of the Reoviridae family) undergo rearrangements of their genomes. This review describes evidence of rearranged genomes in rotaviruses. Their structure and functions are reviewed. Possible mechanisms of their emergence are discussed, and the significance of genome rearrangements for viral evolution is considered.

Animals↗
PubMed1999

Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo.

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5.8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93.5% of T. p. parva isolates examined were detected by probe TPP1 and 81.8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

Animals↗
PubMed1979

The evolution of the long and short repetitive DNA sequences in sea urchins.

The rates of evolution of purified long and short repetitive DNA sequences were examined by hybridisation analysis between the DNAs from several species of sea urchins. We find that the rates of nucleotide substitution are very comparable within mutually retained sequences for the two classes of repetitive DNA. The loss of hybridisable sequences between species also occurs at similar rates among both the short and long repetitive DNA sequences. Between species that separated less than 50 million years ago, hybridisable short repetitive sequences are lost all through the spectrum of reiteration frequencies. The long repeats contain a few sequences which are highly conserved within all of the species examined, and which amount to approximately 1% of the total genome. The short repetitive class, on the other hand, does not seem to contain any such highly conserved elements. The long repetitive sequences internally appear to contain short 'units' of reiteration, which may comprise families within the long repetitive class. We find no evidence to indicate that the majority of long and short repetitive sequences evolve by different mechanisms or at different rates.

Animals↗
PubMed2001

Evolution of gene order conservation in prokaryotes.

BACKGROUND: As more complete genomes are sequenced, conservation of gene order between different organisms is emerging as an informative property of the genomes. Conservation of gene order has been used for predicting function and functional interactions of proteins, as well as for studying the evolutionary relationships between genomes. The reasons for the maintenance of gene order are still not well understood, as the organization of the prokaryote genome into operons and lateral gene transfer cannot possibly account for all the instances of conservation found. Comprehensive studies of gene order are one way of elucidating the nature of these maintaining forces. RESULTS: Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order. CONCLUSIONS: Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.

Conserved Sequence↗
PubMed1994

Evolution rate of hepatitis delta virus RNA isolated in Taiwan.

The complete RNA sequences of hepatitis delta viruses (HDV) isolated at 3 years apart from a chronic delta hepatitis patient in Taiwan were determined. The sequence analysis showed an overall evolution rate of 3.18 x 10(-3) substitutions/nucleotide/year. The evolution rates in different parts of HDV RNA varied. The hypervariable region evolved faster (4.55 x 10(-3) substitutions/nucleotide/year) than the hepatitis delta antigen (HDAg)-coding region (2.60 x 10(-3) substitutions/nucleotide/year) and the autocatalytic region (1.11 x 10(-3) substitutions/nucleotide/year). These data are compatible with the previous finding that the hypervariable region is more divergent than the HDAg-coding region and the autocatalytic regions among the HDV isolates from different geographic areas. No substitution was found in the four previously identified conserved domains of HDV RNA, further confirming their functional importance in viral replication. The evolution rate of this HDV RNA is higher than that determined from the partial RNA sequences of two Japanese HDV isolates and similar to that found in a Lebanon isolate. Further, it was found that this HDV RNA retained the same microheterogeneities at 15 nucleotide positions detected in the RNA 3 years earlier. It is concluded that HDV RNA in patients' serum is extremely heterogeneous, and that the nucleotide substitutions in certain nucleotide positions likely have conferred evolutionary advantages for HDV. Viral sequence evolution is a possible mechanism for chronic HDV infection.

Adult↗
PubMed1998

Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene.

We have sequenced the complete coding region of the Rh blood group gene for mouse and rat and that of Rh-related 50 kD glycoprotein (Rh50) for mouse, rat, and crab-eating macaque. Phylogenetic analyses of Rh and Rh50 amino acid sequences indicate that the Rh50 gene has been evolving about two times more slowly than the Rh blood group gene in both primates and rodents. This conservative nature of the Rh50 gene suggests its relative importance to the Rh blood group gene. The time of gene duplication that produced the Rh and Rh50 genes was estimated to be about 240-310 million years ago. We also conducted window analyses of synonymous and nonsynonymous nucleotide substitutions for those two genes. Some peaks where nonsynonymous substitutions are higher than synonymous ones were located on outer membrane regions. This suggests the existence of positive Darwinian selection on Rh and Rh50 genes through host-parasite interactions.

Animals↗
PubMed1994

Evolutionary conservation of chymotrypsinogen gene: genomic analysis and protein modeling.

Chymotrypsinogen is widely present in various animal pancreases. To study evolutionary relationship of chymotrypsinogen gene in species, we used a cDNA probe of human prechymotrypsinogen to investigate the species distribution of chymotrypsinogen gene, and designed oligodeoxynucleotide primers to investigate the genomic organization in the three domains of active sites. The genomic analyses showed that chymotrypsinogen gene is evolutionary conserved in species. On the basis of the deduced amino acid residues, a three-dimensional model for human chymotrypsinogen was further built by computer graphics. The model showed high similarity to the X-ray crystal structure of bovine chymotrypsinogen A, thus, demonstrated that the three-dimensional structure is more conserved in evolution than protein sequences.

Animals↗
PubMed1993

Concerted evolution in the GAPDH family of retrotransposed pseudogenes.

In murine rodents the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) multigene family includes more than 300 retroprocessed pseudogenes. Its single functional gene encodes GAPDH, an enzyme of glycolysis. Because of its manageable size, this family is a good model for the study of genome cohesion and evolution. By sequence comparison of several GAPDH pseudogenes in Rattus norvegicus and Mus musculus, we have obtained evidence that (i) the GAPDH family still generates new pseudogenes; we note in each species the beginning of a process of species-specific evolution since the pseudogenes of one genus on average cluster more with one another than they do with those of the other genus, and (ii) the GAPDH family contains diversified subfamilies. These findings suggest a certain level of transcription and transposition of the pseudogenes independent of the functional gene which may result from various mechanisms. The homogenization we observe may be due to the pseudogenes themselves (concerted evolution in a strict sense), which explains the occurrence of long-term homogenization of old sequences and subfamily groupings.

Animals↗