PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “sequence evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed1991

Periodicity in DNA coding sequences: implications in gene evolution.

In this paper we have employed Fourier analysis of DNA coding and non-coding sequences in an attempt to identify possible patterns in gene sequences. It was found that while intronic sequences show a rather random pattern, coding sequences show periodicities and in particular a periodicity of 3. We were able to reconstruct such patterns by assuming a gene having one codon occurring in about 40% of the sequence. This could indicate that the predominant presence of codons all starting from the same base could confer the observed periodicities. Indeed, it was found that proteins do obey this rule. Implications of this finding in gene evolution are discussed.

Animals↗
PubMed1978

Evolution of a human Y chromosome-specific repeated sequence.

The structure and evolution of a repetitive sequence on the human Y chromosome has been studied by restriction enzyme analysis of both total DNA and the isolated sequence. The sequence is shown to cross-hybridize to sequences in female DNA forming unstable duplexes. Mouse/human cell hybrids have been used to investigate the pattern of sequence homology on the X chromosome and some autosomes. We conclude that this sequence is related to human satellite III, but shows considerable differences in structure.

Base Sequence↗
PubMed1987

Evolution of P transposable elements: sequences of Drosophila nebulosa P elements.

P elements have been cloned and sequenced from Drosophila nebulosa. Their sequences have diverged less than 6% from P elements of Drosophila melanogaster. However D. nebulosa P elements have nucleotide changes that close all four open reading frames found in the D. melanogaster P element. Microinjection experiments show that D. nebulosa P elements cannot provide transposase function for D. melanogaster P elements, nor are D. nebulosa P elements mobilized by the transposase provided by a D. melanogaster P factor. Three D. nebulosa P elements appear to have integrated into the same position of a complex, centromeric repeated sequence. Comparison of nucleotide sequences suggests that D. nebulosa P elements have diverged upon different pathways from a common ancestor that was 99% homologous to the P elements of D. melanogaster.

Base Sequence↗
PubMed1989

Sequence conservation in Alu evolution.

A statistical analysis of a set of genomic human Alu elements is based on a published alignment and a recent classification of these sequences. After separation of the Alu sequences into families, the consensus sequences of these families are determined, using the correct weighting of the unidirectional decay of CG-dinucleotides. For, the tenfold greater mutation rate at CG's requires separate consideration of an independent clock at every stage of analysis. The distributions of the substitutions with respect to the new consensus sequences, taking the CG and the non-CG-nucleotide positions separately, lie far closer to the expected distributions than the total diversity. Computer analysis of the folding of RNAs derived from these sequences indicates that RNA secondary structure is conserved among Alu families, suggesting its importance for Alu proliferation and/or function. The folding pattern, further substantiated by a number of compensatory mutations, includes secondary structure domains which are homologous to those observed in 7SL RNA and a defined region of interaction between the two Alu subunits. These results are consistent with a model in which a small number of conserved Alu master genes give rise via retroposition to the numerous copies of Alu pseudogenes, that then diversify by random substitution. The master genes appeared at different periods during evolution giving rise to different families of Alu sequences.

Base Composition↗
PubMed1989

Sequence of cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during bromovirus evolution.

The genomic sequence of cowpea chlorotic mottle virus (CCMV) was completed by sequencing biologically active cDNA clones of CCMV RNA2 (2774 bases) and RNA3 (2173 bases). While only the central core of the encoded 94-kDa CCMV 2a protein contains features conserved among known and putative RNA replication proteins from many viruses, both flanking regions of CCMV 2a show substantial similarity to the corresponding protein of the related brome mosaic virus (BMV). The 3a proteins of CCMV and BMV, implicated as contributors to the distinct host specificities of the two viruses, show lower levels of conservation but are still discernibly related throughout. Major differences occur in the organization of noncoding sequences in CCMV and BMV RNA3. With respect to an otherwise similar region preceding the BMV 3a gene, the CCMV RNA3 5' noncoding sequence contains a clearly bounded 111-base insertion that must reflect a sequence rearrangement in evolution of at least one of the two viruses. The presence of a subgenomic promoter-like sequence near the end of the novel CCMV sequence makes the organization of genes in CCMV RNA3 reminiscent of the 3' end of tobacco mosaic virus RNA, suggesting that CCMV or its 3a gene might have been derived from an ancestor with fewer genomic RNAs. Sequence similarities between the CCMV and BMV RNA3 intercistronic regions include the subgenomic mRNA promoter and an oligo(A), but not an intercistronic segment required for BMV RNA3 amplification, implying that replication signals on the two RNA3s may be organized quite differently.

Amino Acid Sequence↗
PubMed1976

DNA sequence arrangement and preliminary evidence on its evolution.

Some recent measurements of the sequence arrangement and evolution of the eukaryotic genome are reviewed. The range of genome sizes and extent of sequence transcribed into nuclear and messenger RNA indicate that the majority of the single copy DNA is not made up of structural genes. The rate of base substitution in the single copy DNA among the primates is similar to that of the codons for certain rapidly changing amino acid residues. This leads to the hypothesis that there is a "basal" rate of change in the genome not strongly affected by selection. The DNA of most higher animals shows a large amount of short period interspersion of repetitive and single copy DNA sequences and a smaller amount of long repetitive regions. The sequence divergence among the short interspersed repetitive sequences is greater than that of the sequences in long repetitive regions. The long repetitive regions are most probably recent additions to the genome and the short interspersed repetitive sequences result from a history of base substitution and translocation. The process of sequence rearrangement appears to be a significant part of the evolution of the genome and may have a much greater effect on the evolution of the phenotype than sequence alteration by base substitution.

Alleles↗
PubMed1978

Instability of plasmid DNA sequences: macro and micro evolution of the antibiotic resistance plasmid R6-5.

Detailed examination of the structure of cloned DNA fragments of the R6-5 antibiotic resistance plasmid has revealed a substantial degree of polynucleotide sequence heterogeneity and indicates that sequence rearrangements in plasmids and possible other replicons occur more frequently than has hitherto been appreciated. The sequences changes in cloned R6-5 fragments were shown in some instances to have occurred prior to cloning, i.e. existing in the original population of R6-5 molecules that was obtained from a single bacterial clone and by several different criteria judged to be homogeneous, and in others to have occurred either during the cloning procedure or during subsequent propagation of hybrid molecules. The molecular changes that are described involved insertion/deletion of the previously characterized IS2 insertion element, formation of a new inverted repeat structure probably by duplication of a preexisting R6-5 DNA sequence, sequence inversion, and loss and gain of restriction endonuclease cleavage sites.

Anti-Bacterial Agents↗
PubMed1976

Sequences of 5S ribosomal RNA from Xenopus mulleri and the evolution of 5S gene-coding sequences.

Sequences for 5S RNA from somatic cells and oocytes of Xenopus mulleri are presented. Comparison with sequences previously given for Xenopus laevis indicates that the somatic 5S RNA genes of each species are more closely related to each other than either is to its own set of oocyte genes, suggesting that somatic and oocyte genes within each species are evolving independently. However, detailed analysis of sequence variants in each species suggests that there is a mechanism which allows occasional genetic exchanges between somatic and oocyte-specific genes. Possible genetic mechanisms which allows such an exchange are discussed.

Animals↗
PubMed1989

Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae.

The genes for the four largest subunits, A, B', B" and C, of the DNA-dependent RNA polymerase were cloned from the extreme halophile Halobacterium halobium and sequenced and their transcription was analyzed. The downstream half of this gene cluster from another extreme halophile Halococcus morrhuae was also cloned, sequenced and its transcription products characterized. The H. halobium genes were transcribed into a common transcript from an upstream promoter in the order B", B', A and C. They are flanked by, and co-transcribed with, two smaller genes coding for 75 and 139 amino acid residues, respectively. Immediately downstream from these genes were two open reading frames that are homologous to ribosomal proteins S12 and S7 from Escherichia coli. In both extreme halophiles these genes were transcribed from their own promoter, but in Hc. morrhuae there was also considerable read-through from the RNA polymerase genes. Sequence alignment studies showed that the combined B" + B' subunits are equivalent to the B subunits of the eukaryotic polymerases I and II and to the eubacterial beta subunit, while the combined A + C subunits correspond to the A subunits of eukaryotic RNA polymerases I, II and III and to the eubacterial beta' subunit. The sequence similarity to the eukaryotic subunits was always much higher than to the eubacterial subunits. Conserved sequence regions within the individual subunits were located which are likely to constitute functionally important domains; they include sites associated with rifampicin and alpha-amanitin binding and two possible zinc binding fingers. Phylogenetic analyses based on sequence alignments confirmed that the extreme halophiles belong to the archaebacterial kingdom.

Archaea↗
PubMed1991

Genomic organization of adrenergic and serotonin receptors in the mouse: linkage mapping of sequence-related genes provides a method for examining mammalian chromosome evolution.

Five sequence-related genes encoding four adrenergic receptors and a serotonin receptor were localized to specific regions of four mouse chromosomes with respect to 11 other genetic markers. Linkage was established by the analysis of the haplotypes of 114 interspecific backcross mice. Adra2r (alpha 2-C10) and Adrb1r (beta 1) receptors mapped to the distal region of mouse chromosome 19. These genes were separated by 2.6 +/- 1.5 cM in a segment of mouse chromosome 19 that has a similar organization of these genes on the long arm of human chromosome 10. The Adra1r (alpha 1B), Adrb2r (beta 2), and Htra1 (5HT1A) genes mapped to proximal mouse chromosome 11, proximal mouse chromosome 18, and distal mouse chromosome 13, respectively. The organization of genes linked to these loci on regions of the three mouse chromosomes is consistent with the organization of homologous human genes on human chromosome 5. These findings further define the relationship of linkage groups conserved during the evolution of the mouse and human genomes. We have identified a region that may have been translocated during evolution and suggest that the human genomic organization of adrenergic receptors more closely resembles that of a putative primordial ancestor.

Animals↗
PubMed1989

Nucleotide sequence, genomic organization and evolution of a major repetitive DNA family in tilapia (Oreochromis mossambicus/hornorum).

A highly repetitive DNA sequence from tilapia (Oreochromis mossambicus/hornorum) has been cloned and sequenced. It is a tandemly arrayed sequence of 237 bp and constitutes 7% of the fish genome. The copy number of the repeat is approximately 3 x 10(5) per haploid genome. DNA sequence analysis of 7 cloned repeats revealed a high degree of conservation of the monomeric unit. Within the monomeric unit, a 9 bp AT rich motif is regularly spaced approximately 30 bp apart and may represent the progenitor of the amplified sequence. One cloned repeat, Ti-14, contained a 30 bp deletion at a position flanked by a 7 bp direct repeat. The Ti-14 sequence appears to have been amplified independently of the major 237 bp tandem array. A higher-order repeat unit, defined by longer-range periodicities revealed by restriction endonuclease digestion, is further imposed on the tandem array.

Animals↗
PubMed1976

Evolution of repeated DNA sequences by unequal crossover.

It is often supposed that highly repetitious DNA's arise only as a result of unusual mechanisms or in response to selective pressure. My arguments and simulations suggest, by contrast, that a pattern of tandem repeats is the natural state of DNA whose sequence is not maintained by selection. The simulations show that periodicities can develop readily from nonreptitious DNA as a result of the random accumulation of random mutations and random homology-dependent unequal crossovers. The lengths of these periodicities, and the patterns of subrepeats within them, would fluctuate in evolution, with the probability of a given pattern being dependent on the unknown exact nature of the crossover mechanism. Qualitatively, then, unequal crossover provides a reasonable and uncontrived explanation for the prevalence of highly repeated sequences in DNA and for the patterns of periodicity they evince.

Animals↗
PubMed1991

Angiosperm origin and early stages of seed plant evolution deduced from rRNA sequence comparisons.

Complete or partial nucleotide sequences of five different rRNA species, coded by nuclear (18S, 5.8S, and 5S) or chloroplast genomes (5S, 4.5S) from a number of seed plants were determined. Based on the sequence data, the phylogenetic dendrograms were built by two methods, maximum parsimony and compatibility. The topologies of the trees for different rRNA species are not fully congruent, but they share some common features. It may be concluded that both gymnosperms and angiosperms are monophyletic groups. The data obtained suggest that the divergence of all the main groups of extant gymnosperms occurred after the branching off of the angiosperm lineage. As the time of divergence of at least some of these gymnosperm taxa is traceable back to the early Carboniferous, it may be concluded that the genealogical splitting of gymnosperm and angiosperm lineages occurred before this event, at least 360 million years ago, i.e., much earlier than the first angiosperm fossils were dated. Ancestral forms of angiosperms ought to be searched for among Progymnospermopsida. Genealogical relationships among gymnosperm taxa cannot be deduced unambiguously on the basis of rRNA data. The only inference may be that the taxon Gnetopsida is an artificial one, and Gnetum and Ephedra belong to quite different lineages of gymnosperms. As to the phylogenetic position of the two Angiospermae classes, extant monocotyledons seem to be a paraphyletic group located near the root of the angiosperm branch; it emerged at the earliest stages of angiosperm evolution. We may conclude that either monocotyledonous characters arose independently more than once in different groups of ancient Magnoliales or that monocotyledonous forms rather than dicotyledonous Magnoliales were the earliest angiosperms. Judging by the rRNA trees, Magnoliales are the most ancient group among dicotyledons. The most ancient lineage among monocotyledons leads to modern Liliaceae.

Base Sequence↗
PubMed1990

Structure and development of rabbit pepsinogens. Stage-specific zymogens, nucleotide sequences of cDNAs, molecular evolution, and gene expression during development.

In order to clarify the structure and development of rabbit pepsinogens, purification and molecular cloning of these proteins were performed at various developmental stages. Several pepsinogens were isolated, and they were classified as pepsinogens F and M, and into pepsinogen groups I, II, and III. The relative levels and specific activities of the various pepsinogens changed significantly during development. Pepsinogens F and M were present only at the early postnatal stage, and their level was higher than those of other pepsinogens at this stage. Pepsinogens in groups I, II, and III were the predominant zymogens at the late postnatal stage. cDNA clones encoding all of these pepsinogens were obtained, with the exception of pepsinogens I and M, and the nucleotide sequences were determined. Each cDNA contained a leader region (signal peptide), a pro-region (activation segment), and a pepsin region, of 15, 44, and 328 residues, respectively, with the exception of the cDNA for pepsinogen F in which the pro- and pepsin regions were composed of 43 and 330 residues, respectively. Pepsinogens in groups II and III exhibited a high degree of similarity with one another, whereas many substitutions were found in pepsinogen F. A unique substitution in the activation segment of pepsinogen F, namely, Gly----Asp at position 21, was found, which made the structural features of this segment more specific. A phylogenic tree was constructed from the differences in nucleotide sequences and showed clearly that each pepsinogen in groups II and III could be classified as pepsinogen A, a major pepsinogen in mammals. Pepsinogen F diverged significantly from these groups and may be a new type of pepsinogen. Northern analysis revealed that the expression of the gene for pepsinogen F was restricted to the early postnatal stage, and the expression of genes for pepsinogens in groups II and III was detected predominantly at later stages, a result that shows the switching of gene expression from fetal pepsinogen to adult pepsinogens during development.

Aging↗
PubMed1990

Sequence of the genome RNA of rubella virus: evidence for genetic rearrangement during togavirus evolution.

The nucleotide sequence of the rubella virus (RUB) genomic RNA was determined. The RUB genomic RNA is 9757 nucleotides in length [excluding the poly(A) tail] and has a G/C content of 69.5%, the highest of any RNA virus sequenced to data. The RUB genomic RNA contains two long open reading frames (ORFs), a 5'-proximal ORF of 6656 nucleotides and a 3'-proximal ORF of 3189 nucleotides which encodes the structural proteins. Thus, the genomic organization of RUB is similar to that of alphaviruses, the other genus of the Togavirus family, and the 5'-proximal ORF of RUB therefore putatively codes for the nonstructural proteins. Sequences homologous to three regions of nucleotide sequence highly conserved among alphaviruses (a stem-and-loop structure at the 5' end of the genome, a 51-nucleotide conserved sequence near the 5' end of the genome, and a 20-nucleotide conserved sequence at the subgenomic RNA start site) were found in the RUB genomic RNA. Amino acid sequence comparisons between the nonstructural ORF of RUB and alphaviruses revealed only one short (122 amino acids) region of significant homology, indicating that these viruses are only distantly related. This region of homology is located at the NH2 terminus of nsP3 in the alphavirus genome. The RUB nonstructural protein ORF contains two global amino acid motifs conserved in a large number of positive-polarity RNA viruses, a motif indicative of helicase activity and a motif indicative of replicase activity. The order of the helicase motif and the nsP3 homology region in the RUB genome is reversed with respect to the alphavirus genome indicating that a genetic rearrangement has occurred during the evolution of these viruses.

Amino Acid Sequence↗
PubMed1979

Analysis of the constancy of DNA sequences during development and evolution of the nematode Caenorhabditis elegans.

In order to test for the occurrence of rearrangements in DNA during development and to assess the rate of DNA divergence during evolution, we have compared restriction fragments derived from DNA from four sources: sperm cells and somatic tissues of one strain of the nematode Caenorhabditis elegans, somatic tissues of a second strain of the same species, and whole animals of a closely related species. Restriction fragments were detected by hybridizing radioactive cloned fragments to restriction digests that had been fractionated by size on agarose gels and transferred to nitrocellulose sheets. In this way, approximately 50 BamHI restriction fragments were visualized and compared. Fragments from sperm and somatic DNAs were found to be identical; 15% differed in size between the two strains. Little cross homology was found between the two species. We conclude that, if rearrangements occur in C. elegans DNA during development, they must affect fewer than a few percent of the restriction fragments or restriction sites. The difference found between the two strains and the two species is surprisingly great.

Animals↗
PubMed1992

The mechanisms controlling ribosomal protein L1 pre-mRNA splicing are maintained in evolution and rely on conserved intron sequences.

Sequences corresponding to the third intron of the X.laevis L1 ribosomal protein gene were isolated from the second copy of the X.laevis gene and from the single copy of X.tropicalis. Sequence comparison revealed that the three introns share an unusual sequence conservation which spans a region of 110 nucleotides. In addition, they have the same suboptimal 5' splice sites. The three introns show similar features upon oocyte microinjection: they have very low splicing efficiency and undergo the same site specific cleavages which lead to the accumulation of truncated molecules. Computer analysis and RNAse digestions have allowed to assign to the conserved region a specific secondary structure. Mutational analysis has shown that this structure is important for conferring the cleavage phenotype to these three introns. Competition experiments show that the cleavage phenotype can be prevented by coinjection of excess amounts of homologous sequences.

Animals↗