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At least 433 records · Page 24Linked to original sources
PubMed1994

Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny.

Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly conserved regions of exons in order to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six species of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times < or = 40-50 Mya. We sequenced one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for comparison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be of limited use because they were paralogous with the gene in the outgroup. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA sequence divergence increased linearly with time < or = 40-50 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the allele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the consequences of a higher mutation rate rather than to a lower effective population size of mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences of individual scnDNA sequences, phylogenetically informative variation was insufficient to obtain robust phylogenies. However, the combined scnDNA sequences produced a well-supported phylogeny congruent with that derived from mtDNA. This analysis illustrates the high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining information from multiple short scnDNA sequences obtained using broadly applicable primers.

Animals↗
PubMed1981

On the hydrophobic nature of signal sequences.

A number of signal sequences, prokaryotic as well as eukaryotic, have been analyzed in terms of gross amino acid composition and hydrophobicity. It is shown that the amino acid composition of the hydrophobic core can be well reproduced in a computer simulation of signal sequence 'evolution' with selection operating on the mean hydrophobicity of the sequence and the non-occurrence of charged residues. The calculated hydrophobicities are interpreted in terms of a model in which the hydrophobic part of the signal sequence partitions directly into the membrane interior, thereby making further translocation of the growing nascent chain possible.

Amino Acids↗
PubMed1994

Rapid evolution of a protein in vitro by DNA shuffling.

DNA shuffling is a method for in vitro homologous recombination of pools of selected mutant genes by random fragmentation and polymerase chain reaction (PCR) reassembly. Computer simulations called genetic algorithms have demonstrated the importance of iterative homologous recombination for sequence evolution. Oligonucleotide cassette mutagenesis and error-prone PCR are not combinatorial and thus are limited in searching sequence space. We have tested mutagenic DNA shuffling for molecular evolution in a beta-lactamase model system. Three cycles of shuffling and two cycles of backcrossing with wild-type DNA, to eliminate non-essential mutations, were each followed by selection on increasing concentrations of the antibiotic cefotaxime. We report here that selected mutants had a minimum inhibitory concentration of 640 micrograms ml-1, a 32,000-fold increase and 64-fold greater than any published TEM-1 derived enzyme. Cassette mutagenesis and error-prone PCR resulted in only a 16-fold increase.

Base Sequence↗
PubMed2001

Structure and expression of the scallop Omega-crystallin gene. Evidence for convergent evolution of promoter sequences.

Omega-crystallin of the scallop lens is an inactive aldehyde dehydrogenase (1A9). Here we have cloned the scallop Omega-crystallin gene. Except for an extra novel first exon, its 14-exon structure agrees well with that of mammalian aldehyde dehydrogenases 1, 2, and 6. The -2120/+63, -714/+63, and -156/+63 Omega-crystallin promoter fragments drive the luciferase reporter gene in transfected alphaTN4-1 lens cells and L929 fibroblasts but not in Cos7 cells. Putative binding sequences for cAMP-responsive element-binding protein (CREB)/Jun, alphaACRYBP1, AP-1, and PAX-6 in the Omega-crystallin promoter are surprisingly similar to the cis-elements used for lens promoter activity of the mouse and chicken alphaA-crystallin genes, which encode proteins homologous to small heat shock proteins. Site-specific mutations in the overlapping CREB/Jun and Pax-6 sites abolished activity of the Omega-crystallin promoter in transfected cells. Gel shift experiments utilizing extracts from the alphaTN4-1, L929, and Cos7 cells and the scallop stomach and oligonucleotides derived from the putative binding sites of the Omega-crystallin promoter showed complex formation. Gel shift experiments showed binding of recombinant Pax-6 and CREB to their respective sites. Our data suggest convergent evolutionary adaptations that underlie the preferential expression of crystallin genes in the lens of vertebrates and invertebrates.

Animals↗
PubMed1995

Simulating efficiently the evolution of DNA sequences.

Two menu-driven FORTRAN programs are described that simulate the evolution of DNA sequences in accordance with a user-specified model. This general stochastic model allows for an arbitrary stationary nucleotide composition and any transition-transversion bias during the process of base substitution. In addition, the user may define any hypothetical model tree according to which a family of sequences evolves. The programs suggest the computationally most inexpensive approach to generate nucleotide substitutions. Either reproducible or non-repeatable simulations, depending on the method of initializing the pseudo-random number generator, can be performed. The corresponding options are offered by the interface menu.

Algorithms↗
PubMed2003

Birth and death of orphan genes in Rickettsia.

The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphan genes, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. Of the Rickettsia conorii orphans examined in this study, 80% were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient open reading frames. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes.

Base Sequence↗
PubMed1993

Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.).

Copia-like retrotransposable elements were identified in allotetraploid cotton, Gossypium hirsutum, and two species representing its diploid progenitors, G. herbaceum and G. raimondii. These elements are present in high copy number in all three species. Because the two diploid genomic groups have been isolated on opposite sides of the world for 6-11 million years, horizontal transfer of elements between these species is highly unlikely. Elements were intensively sampled to generate a model of copia-like retrotransposable element evolution in systems where vertical transmission is the sole probable means of descent. Copia-like retrotransposon diversity is equally great in all three Gossypium species. Despite this high heterogeneity, analysis of 89 partial reverse transcriptase sequences resulted in the recognition of nine sharply differentiated retrotransposon lineages, each containing elements that share high sequence similarity. No evidence of horizontal transfer from other taxa was obtained. Phylogenetic analyses demonstrate that element topologies are incongruent with Gossypium phylogeny. Consideration of processes that obscure phylogenetic reconstruction of multigene families (including sampling error, variable degrees of orthology and paralogy, differential lineage age and lineage loss and/or proliferation) demonstrates that incongruence between organismal and retrotransposon trees is expected under conditions in which vertical processes are the sole means of transmission. Identification of closely related elements between species allowed rates of copia-like retrotransposon sequence evolution to be estimated as approximately 10(-9) nucleotide substitutions/site/year. These rates are consistent with the interpretation that these retrotransposons have been evolving under functional constraints for most of the time frame bracketed by the species studied. Extrapolation of these results to previous studies that sampled from more highly divergent taxa indicates that horizontal transfer need not be invoked to explain observed phylogenetic patterns.

Amino Acid Sequence↗
PubMed1996

Mitochondrial gene sequences and the molecular systematics of the artiodactyl subfamily bovinae.

Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla. The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). Although the phylogenetic analyses grouped Bison as sister to Bos, the genus Bison was paraphyletic, with the American bison being most closely related to species of Bos rather than to the European bison. COII data also supported a close relationship between African (Syncerus) and Asian (bubalus) buffaloes, the monophyly of the tribe Bovini, and a sister-group relationship between the tribes Bovini and Boselaphini. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa.

Animals↗
PubMedDate not supplied

Evidence on human origins from haemoglobins of African apes.

Molecular data have influenced views concerning human origins, first, by supporting the genealogical classification of Pan (chimpanzee) and Gorilla with Homo rather than with Pongo (orangutan) and, second, by suggesting that only a few million years separate humans and chimpanzees from their last common ancestor. Indeed, the cladistic distances in phylogenetic trees constructed from amino acid sequence data, on detecting many superimposed mutations, yielded a 'molecular-clock' divergence date between Homo and Pan of only 1-1.5 Myr BP. This date, which is even more recent than (4.2-5.3 Myr BP) calculated using phenetic distances from immunological and DNA-hybridization comparisons (Table 1), is too near the present considering the existence of 3-4 Myr-old fossils of bipedal human ancestors (and a 5.5 Myr-old jaw fragment assigned to Australopithecus). Perhaps decelerated sequence evolution occurred; alternatively, hominoid distances could have been underestimated, because chimpanzee and gorilla were represented mostly by sequences inferred from peptide amino acid compositions, as was the case for their haemoglobins. To help rectify this situation we report here the rigorously determined alpha- and beta-haemoglobin amino acid sequences not only of chimpanzee (Pan troglodytes) and Gorilla gorilla but also pygmy chimpanzee (Pan paniscus). Our findings favour the explanation of decelerated evolution and point to selection preserving perfected haemoglobin molecules.

Amino Acid Sequence↗
PubMed1994

Parallel evolution in the V3 region of HIV type 1 after infection of hemophiliacs from a homogeneous source.

To determine the genetic diversification in the highly functional V3 loop, we followed up five hemophiliacs who were infected by a homogeneous HIV-1 population from a contaminated clotting factor lot. Initially, all patients displayed identical DNA sequences in this part of the proviral env gene. Therefore, this unique outbreak allows us to investigate the biological and genetic development of a common ancestor virus in different patients. A high degree of homology is maintained in the predominant sequences from 5 until 35 months after seroconversion. Only one patient showed a remarkable diversification 3 years postinfection. However, these genetic changes in the V3 region were not associated with disease progression. Discontinuous sequence changes were observed mainly in a region downstream of the V3 loop. Two positions in particular are involved in a sequence evolution within the V3 loop leading to the same amino acids in different patients. These directed changes occurred at sites that are reported to be critical for the specificity of antibodies (position 308) and viral cytopathicity (position 324). However, the parallel evolution was associated neither with differentiation of the viral phenotype nor with progression of the disease.

Amino Acid Sequence↗
PubMed1995

The appearance of proopiomelanocortin early in vertebrate evolution: cloning and sequencing of POMC from a Lamprey pituitary cDNA library.

A proopiomelanocortin (POMC)-like hormone has been cloned and sequenced from a pituitary cDNA library of upstream migrant (prespawning) sea lamprey, Petromyzon marinus. The clone, designated LPP-1, consisted of 986 nucleotides, with an open reading frame of 277 amino acids, including a signal peptide of 22 amino acids. Like POMCs from more recently evolved vertebrates, lamprey POMC contained domains which corresponded to alpha-MSH, ACTH, and beta-endorphin. However, sequences corresponding to gamma- and beta-MSH are absent or likely nonfunctional, respectively, in this cDNA. Northern blot analyses showed low but detectable expression levels of LPP-1 in larvae and strong expression in parasitic adults and prespawning animals. These observations indicate that a recognizable POMC, distinct from proenkephalin, has an ancient lineage within subphylum Vertebrata, likely dating back to the last common ancestor of the lamprey and gnathostome lines.

Adrenocorticotropic Hormone↗
PubMed1999

Evolution of protein sequences and structures.

The relationship between sequence similarity and structural similarity has been examined in 36 protein families with five or more diverse members whose structures are known. The structural similarity within a family (as determined with the DALI structure comparison program) is linearly related to sequence similarity (as determined by a Smith-Waterman search of the protein sequences in the structure database). The correlation between structural similarity and sequence similarity is very high; 18 of the 36 families had linear correlation coefficients r>/=0.878, and only nine had correlation coefficients r</=0.815. Inclusion of higher-order terms in the structure/sequence relationship improved the fit by less than 7% in 27 of the 36 families. Differences in sequence/structure correlations are distributed evenly among the four protein structural classes, alpha, beta, alpha/beta, and alpha+beta. While most protein families show high correlations between sequence similarity and structural similarity, the amount of structural change per sequence change, i.e. the structural mutation sensitivity, varies almost fourfold. Protein families with high and low structural mutation sensitivity are distributed evenly among protein structure classes. In addition, we did not detect strong correlations between structural mutation sensitivity and either protein family mutation rates or protein size. Our results are more consistent with models of protein structure that encode a protein family's fold throughout the protein sequence, and not just in a few critical residues.

Amino Acid Sequence↗
PubMed2001

Pruned median networks: a technique for reducing the complexity of median networks.

Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not tree-like. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.

Base Sequence↗
PubMed1972

Evolution of neurophysin proteins: the partial sequence of bovine neurophysin-I (vasopressin-oxytocin-carrier proteins-automated amino-acid-sequence analysis-homology-protein evolution).

The sequence of the first 50 amino-acid residues of bovine neurophysin-I was determined. A comparison of this sequence with that of the 97-residue bovine neurophysin-II and the 92-residue porcine neurophysin-I molecules reveals a high degree of homology among these proteins. It is suggested that the binding site of neurophysin proteins for neurohypophyseal hormones is located in the middle portion of these molecules, where their sequences are virtually identical. The sequence data, as well as the occurrence of at least two neurophysins in both the pig and the cow, suggest that each species inherited at least two structural genes controlling the synthesis of these proteins. The most striking finding in the study was the observation of internal sequence homologies within the neurophysins. This result implies that these molecules arose by way of a series of partial gene duplications of a primitive gene that coded for a smaller ancestral protein.

Acetamides↗
PubMed2004

Bovine respiratory syncytial virus strains currently circulating in the Czech Republic are most closely related to Danish strains from 1995.

In this study we showed a high degree of genetic homogeneity among recently (2002-2003) circulating Bovine respiratory syncytial virus (BRSV) strains in cattle population in the Czech Republic. These strains are in a phylogenetic tree more closely related to the Danish strains from 1995 than to the Czech strain VS97 from 1997 that shares the highest similarity with the French strain F1 and the Belgian strain P10. From the sequence analysis we deduce that the revealed high diversity between BRSV strains from 2002-2003 and those from 1997, at both nucleotide (0-11.4%) and amino acid (0-21%) level, is more likely due to distinct sources of the virus strains than to the sequence evolution.

Amino Acid Sequence↗
PubMed1988

The rat gene encoding neurotensin and neuromedin N. Structure, tissue-specific expression, and evolution of exon sequences.

Recombinant DNA clones encoding the neurotensin/neuromedin N precursor protein have been isolated from both bovine hypothalamus cDNA and rat genomic libraries using a heterologous canine cDNA probe. Nucleotide sequence analysis of these clones and comparison with the previously determined canine sequence has revealed that 76% of the amino acid residues are conserved in all three species. The protein precursor sequences predicted from bovine hypothalamus and canine intestine cDNA clones vary at only 9 of 170 amino acid residues suggesting that within a species identical precursors are synthesized in both the central nervous system and intestine. The rat gene spans approximately 10.2 kilobases (kb) and is divided into four exons by three introns. The neurotensin and neuromedin N coding domains are tandemly positioned on exon 4. RNA blot analysis has revealed that the rat gene is transcribed to yield two distinct mRNAs, 1.0 and 1.5 kb in size, in all gastrointestinal and all neural tissues examined except the cerebellum. There is a striking variation in the relative levels of these two mRNAs between brain and intestine. The smaller 1.0-kb mRNA greatly predominates in intestine while both mRNA species are nearly equally abundant in hypothalamus, brain stem, and cortex. Sequence comparisons and RNA blot analysis indicate that these two mRNAs result from the differential utilization of two consensus poly(A) addition signals and differ in the extent of their 3' untranslated regions. The relative combined levels of the mRNAs in various brain and intestine regions correspond roughly with the relative levels of immunologically detectable neurotensin except in the cerebral cortex where mRNA levels are 6 times higher than anticipated.

Amino Acid Sequence↗
PubMed1994

Mitochondrial DNA variation and the evolution of Robertsonian chromosomal races of house mice, Mus domesticus.

The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time.

Animals↗