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PubMed2005

Conservation versus parallel gains in intron evolution.

Orthologous genes from distant eukaryotic species, e.g. animals and plants, share up to 25-30% intron positions. However, the relative contributions of evolutionary conservation and parallel gain of new introns into this pattern remain unknown. Here, the extent of independent insertion of introns in the same sites (parallel gain) in orthologous genes from phylogenetically distant eukaryotes is assessed within the framework of the protosplice site model. It is shown that protosplice sites are no more conserved during evolution of eukaryotic gene sequences than random sites. Simulation of intron insertion into protosplice sites with the observed protosplice site frequencies and intron densities shows that parallel gain can account but for a small fraction (5-10%) of shared intron positions in distantly related species. Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation.

Animals↗
PubMed2002

Lack of impact of CYP1A2 genetic polymorphism (C/A polymorphism at position 734 in intron 1 and G/A polymorphism at position -2964 in the 5'-flanking region of CYP1A2) on the plasma concentration of haloperidol in smoking male Japanese with schizophrenia.

The impact of genetic polymorphism of CYP1A2 that are related to the induction of the isozyme on the plasma levels of haloperidol (HAL) in 40 male smokers with schizophrenia was investigated. A point mutation from C to A in intron 1 at position 734 and a point mutation from G to A at position -2964 in the 5'-flanking region of CYP1A2 were identified by polymerase chain-reaction-restricted fragment length polymorphism method. Regarding C/A polymorphism in intron 1 at position 734, no significant difference was found in the plasma concentrations of HAL corrected for dose and weight among the subjects with A/A (n = 21), A/C (n = 14) and C/C (n = 5) genotypes (one-way analysis of variance: 63.1 +/- 18.5, 47.8 +/- 12.5 and 50.8 +/- 15.1 ng/ml/mg/kg, respectively, F(2,37) = 2.556, P = .09). Regarding G/A polymorphism at position -2964 in the 5'-flanking region, no significant difference was found in the plasma concentrations of HAL corrected for dose and weight between subjects with G/G (n = 24) and G/A (n = 15) (two-tailed t test: G/G and G/A = 51.2 +/- 16.6 and 59.0 +/- 17.6 ng/ml/mg/kg, respectively, df = 28, P = .22). The present study suggests that the genotyping of CYP1A2 cannot predict the steady state plasma levels of HAL in male smoking schizophrenics.

5' Flanking Region↗
PubMed2000

Molecular characterization of actin genes from homobasidiomycetes: two different actin genes from Schizophyllum commune and Suillus bovinus.

The actin-encoding genes Scact1 and Scact2 of the homobasidiomycete Schizophyllum commune are the first actin genes isolated from higher filamentous fungi. Their isolation shows that homobasidiomycetes have two actin encoding genes instead of one typical to yeasts and filamentous ascomycetes. This result was further confirmed by cloning two actin encoding genes, Sbact1 and Sbact2, from another homobasidiomycete Suillus bovinus. The comparison of the genomic and cDNA sequences of the actin genes showed that Scact1 and Scact2 genes of S. commune contain seven introns, five of which are at the same position in the two genes while S. bovinus actin genes contain nine similarly positioned introns. In the four genes, five intron positions are shared, which indicates a close relationship between the actin encoding genes from S. commune and S. bovinus. Northern hybridization and analysis of two-dimensional immunoblots showed a difference in the expression levels between the two actin genes in each fungus. No actin protein could be detected from S. commune Scact2. The deduced amino acid sequence of the Scact2 gene also differs considerably from any other known actin protein. These data suggest that the Scact2 gene either has a special as yet unidentified function in S. commune life cycle or is a transcribed but no longer translated pseudogene. Scact2 gene has a putative microORF (short open reading frame) and Scact1 gene an intron in the 5'-untranslated region, which could reduce the translational efficiency and increase the transcriptional efficiency of the Scact2 and Scact1 genes, respectively. During mating in S. commune or at formation of ectomycorrhiza in S. bovinus, the expression of actin genes was similar to that in vegetative hyphae. This result suggests that the reorganization of actin cytoskeleton in response to extra- and intracellular signals in higher filamentous fungi could be directly regulated by members of signalling pathways well characterized in yeast and mammalian cells.

Actins↗
PubMed2005

Spectrum of splicing errors caused by CHRNE mutations affecting introns and intron/exon boundaries.

BACKGROUND: Mutations in CHRNE, the gene encoding the muscle nicotinic acetylcholine receptor epsilon subunit, cause congenital myasthenic syndromes. Only three of the eight intronic splice site mutations of CHRNE reported to date have had their splicing consequences characterised. METHODS: We analysed four previously reported and five novel splicing mutations in CHRNE by introducing the entire normal and mutant genomic CHRNEs into COS cells. RESULTS AND CONCLUSIONS: We found that short introns (82-109 nucleotides) favour intron retention, whereas medium to long introns (306-1210 nucleotides) flanking either or both sides of an exon favour exon skipping. Two mutations are of particular interest. Firstly, a G-->T substitution at the 3' end of exon 8 predicts an R286M missense mutation, but instead results in skipping of exon 8. In human genes, a mismatch of the last exonic nucleotide to U1 snRNP is frequently compensated by a matching nucleotide at intron position +6. CHRNE intron 8 has a mismatch at position +6, and accordingly fails to compensate for the exonic mutation at position -1. Secondly, a 16 bp duplication, giving rise to two 3' splice sites (g.IVS10-9_c.1167dup16), results in silencing of the downstream 3' splice site. This conforms to the scanning model of recognition of the 3' splice site, which predicts that the first "ag" occurring after the branch point is selected for splicing.

Adult↗
PubMed1998

Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.

We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero introns originally present in the progenote, while almost all of the remaining intron positions correspond to introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the introns-early/introns-late debate.

Animals↗
PubMed1995

Characterization and chromosomal localization of ELANH2, the gene encoding human monocyte/neutrophil elastase inhibitor.

Human monocyte/neutrophil elastase inhibitor (HEI) is a protease inhibitor of the serpin superfamily that rapidly inactivates neutrophil elastase, proteinase-3, and possibly cathepsin-G in vitro and, by regulating these potent proteases, is thought to prevent tissue damage at inflammatory sites. The HEI gene (ELANH2) was characterized by amplifying intron regions using cDNA-specific primers. Intron positions of ELANH2 were found to be homologous to intron positions in the genes for the serpin molecules chicken ovalbumin and human plasminogen activator inhibitor-2 (PLANH2). Because serpin superfamily genes in general have widely different organizational patterns, the shared organization of these genes strengthens the evidence that they form a subgroup or family, the "ovalbumin-related serpin" ("Ov-serpin") family. By amplifying DNA of a somatic cell hybrid panel, ELANH2 was unambiguously localized to chromosome 6. The use of a panel of radiation and somatic cell hybrids specific for chromosome 6 refined the localization of ELANH2 to the short arm telomeric of D6S89, F13A, and D6S202 at 6p24-pter. Another Ov-serpin gene PI6 (placental thrombin inhibitor) was colocalized to the same region, thus defining an Ov-serpin locus on chromosome 6 in addition to the previously defined PLANH2-containing Ov-serpin locus on chromosome 18.

Base Sequence↗
PubMed1988

Vestiges of lost introns in the thermal stability map of DNA.

The absence of introns in prokaryotic genes has been explained by intron loss on various bases. Here we report another piece of evidence on intron loss, which was found in the thermal stability map of DNA. We calculated the local melting temperature of cDNA sequences and found that (i) gaps in thermal stability tend to occur near intron positions with a statistical significance, and (ii) one-third of the gaps far from intron positions can be assigned to lost introns. From these results we conclude that the gaps of thermal stability in protein coding regions are the vestiges of lost introns.

Animals↗
PubMed1997

Molecular cloning, genomic organization, and developmental regulation of a novel receptor from Drosophila melanogaster structurally related to members of the thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone/choriogonadotropin receptor family from mammals.

Using oligonucleotide probes derived from consensus sequences for glycoprotein hormone receptors, we have cloned an 831-amino acid residue-long receptor from Drosophila melanogaster that shows a striking structural homology with members of the glycoprotein hormone (thyroid-stimulating hormone (TSH); follicle-stimulating hormone (FSH); luteinizing hormone/choriogonadotropin (LH/CG)) receptor family from mammals. This homology includes a very large, extracellular N terminus (20% sequence identity with rat TSH, 19% with rat FSH, and 20% with the rat LH/CG receptor) and a seven-transmembrane region (53% sequence identity with rat TSH, 50% with rat FSH, and 52% with the rat LH/CG receptor). The Drosophila receptor gene is >7.5 kilobase pairs long and contains 17 exons and 16 introns. Seven intron positions coincide with introns in the mammalian glycoprotein hormone receptor genes and have the same intron phasing. This indicates that the Drosophila receptor is evolutionarily related to the mammalian receptors. The Drosophila receptor gene is located at position 90C on the right arm of the third chromosome. The receptor is strongly expressed starting 8-16 h after oviposition, and the expression stays high until after pupation. Adult male flies express high levels of receptor mRNA, but female flies express about 6 times less. The expression pattern in embryos and larvae suggests that the receptor is involved in insect development. This is the first report on the molecular cloning of a glycoprotein hormone receptor family member from insects.

Amino Acid Sequence↗
PubMed1992

The P-glycoprotein gene family of Caenorhabditis elegans. Cloning and characterization of genomic and complementary DNA sequences.

P-glycoproteins, encoded by families of evolutionarily conserved genes, can confer a multidrug-resistant phenotype to mammalian tumor cells. To obtain more information on their functions in normal cells we have cloned genomic and complementary DNA sequences of four P-glycoprotein gene homologs of the genetically well-characterized nematode Caenorhabditis elegans, termed pgp-1, pgp-2, pgp-3 and pgp-4, respectively. The genes were physically mapped on chromosome IV (pgp-1), I (pgp-2) and X (pgp-3 and pgp-4). Phenotypic mutants corresponding to these loci have not yet been described. Two of the genes, pgp-1 and pgp-3, were analyzed in detail. They are predicted to encode ATP-binding membrane-spanning proteins of 1321 and 1254 amino acid residues, respectively, with the characteristic features shared by most P-glycoproteins described thus far. Intra-species divergence of P-glycoprotein genes is more pronounced in C. elegans than in mammals. Only 40% of the amino acids of pgp-1 and pgp-3 are identical, in contrast to 77% identity between human MDR1 and MDR3. pgp-1 consists of 14 exons, pgp-3 of 13. The two genes share only one intron position, whereas they share four (pgp-1) and five (pgp-3) intron positions with mammalian P-glycoprotein genes. pgp-1, pgp-2, and pgp-3 are transcribed into low abundance mRNAs in wild-type nematodes. pgp-1 and pgp-3 mRNAs have the trans-spliced leader SL1 at their 5' ends. Arsenite, emetine and actinomycin D drugs did not increase the steady state levels of pgp mRNA, unlike in some mammalian cell types. Heat shock disturbed trans as well as cis-splicing of pgp-1 and led to the accumulation of partially processed pgp-1 RNA. Thus, in C. elegans these genes are not induced in the context of a general stress response, as has been proposed for mammalian P-glycoprotein genes in certain tissues.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1993

The origin of the bifunctional dihydrofolate reductase-thymidylate synthase isogenes of Arabidopsis thaliana.

In most prokaryotic and eukaryotic organisms dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are encoded by independent genes. Evidence is presented here that the higher plant Arabidopsis thaliana has two bifunctional DHFR-TS genes. The structure of the genes, DHFR at the amino terminus and TS at the carboxy terminus, is identical to their organization in protozoa, the only other known organisms with bifunctional genes. Sequence alignments suggest that the bifunctional genes from protozoa and higher plants may have different evolutionary origins. The positions of the introns support the complementary hypothesis that the DHFR domain of the bifunctional plant genes and the monofunctional DHFR gene of vertebrates derive from a common, intron-containing progenitor, although the structure (bifunctional or monofunctional) of the ancestral gene remains indeterminate. Comparison of the two bifunctional genes of Arabidopsis indicates that the DHFR and TS domains evolved at different rates; each following the evolutionary history of their monofunctional counterparts. In contrast to the DHFR domain, the evolution of the TS domain shows a higher level of nucleotide and amino acid sequence conservation, but a remarkable variability in the intron positions.

Amino Acid Sequence↗
PubMed2003

Genes coding for intermediate filament proteins: common features and unexpected differences in the genomes of humans and the teleost fish Fugu rubripes.

We screened the genomic sequences of the teleost fish Fugu rubripes for genes that encode cytoplasmic intermediate filament (IF) proteins. Here, we compare the number of genes per subfamily (I to IV) as well as the gene mapping in the human and fish genomes. There are several unexpected differences. F. rubripes has a sizeable excess of keratin type I genes over keratin type II genes. Four of the six keratin type II genes map close to four keratin type I genes. Thus, a single keratin II gene cluster (as in mammals) seems excluded. Although a continuous genome sequence is not yet available for F. rubripes, it is difficult to see how all 19 keratin type I genes can be collected as in the human genome into a single cluster without the presence of type II genes and various unrelated genes. F. rubripes has more type III and type IV genes than humans. Some of the type IV genes acquired additional novel intron positions. One gene even harbors (in addition to the two type IV introns) three novel introns and three introns usually present only in mammalian and F. rubripes type I-III genes. This mixture of type IV and type I-III intron positions poses a problem for the traditional view that the first type IV gene arose in evolution by a mRNA-mediated translocation event. In the 42 F. rubripes genes analysed here, there are several differences in intron patterns compared with mammalian genes. Most correspond to additional introns in the fish genes. A search for genes encoding nuclear lamins reveals the four established fish lamins (A, B1, B2 and LIII) as well as an unexpected second lamin A.

Amino Acid Sequence↗
PubMed1989

Mutational analysis of the interactions between U1 small nuclear RNA and pre-mRNA of yeast.

In recent experiments we have used the power of yeast genetics to study U1 small nuclear RNA (snRNA): pre-messenger RNA (pre-mRNA) base pairing interactions [Séraphin et al. EMBO J. 7 (1988) 2533-2538]. Here we extend these observations to other potential U1 snRNA: pre-mRNA pairings. We show that several U1 snRNA mutants are viable. Using these U1 mutant strains we demonstrate further a base-pairing interaction between U1 snRNA position 3 and intron position 6. However, this interaction is only detected with a poor splicing substrate containing branchpoint mutations. These results provide information on the mechanism of 5' splice site-branch point interaction. We also propose several models which may explain why the sequence of the 5' end of the U1 snRNA is conserved among organisms as divergent as man and yeast.

Animals↗
PubMed1996

Molecular evolution of maize catalases and their relationship to other eukaryotic and prokaryotic catalases.

We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases. These sequences were also compared with other eukaryotic and prokaryotic catalases. Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups. The first, and major, group includes maize Cat1, barley Cat1, rice CatB, and most of the dicot catalases. The second group is an apparent dicot-specific catalase group encompassing the tobacco Cat2 and tomato Cat. The third is a monocot-specific catalase class including the maize Cat3, barley Cat2, and rice CatA. The maize Cat2 gene is loosely related to the first group. The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases. Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene. The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence.

Catalase↗
PubMed1992

Characterization of the human nestin gene reveals a close evolutionary relationship to neurofilaments.

Multipotential stem cells in the neural tube give rise to the different neuronal cell types found in the brain. Abrupt changes in intermediate filament gene expression accompany this transition out of the precursor state: transcription of the intermediate filament nestin is replaced by that of the neurofilaments. In order to identify human neural precursor cells, and to learn more about the evolution of the intermediate filaments expressed in the central nervous system, we have isolated the human nestin gene. Despite considerable divergence between the human and rat nestin genes, in particular in the repetitive parts of the carboxy-terminal region, the positions of the introns are perfectly conserved. Two of the three intron positions are also shared by the neurofilaments, but not by other classes of intermediate filaments. This implies that nestin and the neurofilaments had a common ancestor after branching off from the other classes of intermediate filaments, and that nestin separated from the neurofilament branch before the different neurofilament genes diverged. The characterization of human nestin also facilitates the identification of human multipotential neural precursor cells. This will be of importance for central nervous system (CNS) tumor diagnosis and transplant-based clinical approaches to human neurodegenerative diseases.

Amino Acid Sequence↗
PubMed2002

Intron gain and loss in the evolution of the conserved eukaryotic recombination machinery.

Intron conservation, intron gain or loss and putative intron sliding events were determined for a set of three genes (SPO11, MRE11 and DMC1) involved in basic aspects of recombination in eukaryotes. These are ancient genes and present in nearly all of the major kingdoms. MRE11 is of bacterial origin and can be found in all kingdoms. DMC1 is a specialized homolog of the bacterial RecA protein, whereas the SPO11 gene is of archaebacterial origin. Only unique homologs of SPO11 are found in animals and fungi whereas three distantly related SPO11 copies are present in plant genomes. A comparison of the respective intron positions and phases of all genes was performed, demonstrating that a quarter of the intron positions were perfectly conserved over more than 1 000 000 000 years. Regarding the remaining three quarters of the introns we found insertions to be about three times more frequent than deletions. Aligning the introns of the three different SPO11 homologs of Arabidopsis thaliana we propose a conclusive model of their evolution. We postulate that at least one duplication event occurred shortly after the divergence of plants from animals and fungi and that a respective homolog has been retained in a protist group, the apicomplexa.

Arabidopsis↗
PubMed2003

Five-group distribution of the Shaker-like K+ channel family in higher plants.

In higher plants, potassium channels of the Shaker family have been shown to play crucial roles in the uptake of K(+) from the soil solution and subsequent transport of this ion at the cell, tissue, and organ levels. In the model plant Arabidopsis thaliana, this family is composed of nine members, which are the best characterized among plant channels at the protein, gene, and functional property levels. Plant Shaker channels share a common structure: a hydrophobic core composed of six transmembrane segments, a long cytoplasmic C-terminal region harboring a putative cyclic nucleotide binding domain, and a K(HA) domain. Many channels also contain an ankyrin domain between the putative cyclic nucleotide binding domain and the K(HA) domain. The analysis of 44 Shaker channels from plants revealed a five-group classification. The members of each group share high sequence and structure similarities. This grouping also correlates with the diversification of the functional properties of the proteins, as members of an individual group have roughly the same electrophysiological characteristics. Analysis of the intron positions showed that the gene structures are also quite well conserved within the five groups. A correlation linking the evolution of the sequences and the positioning of the introns was established. Finally, a moss sequence provided additional clues about the hypothetical structure of an ancestor of the present channels and suggested that the diversification of plant Shaker channels happened before the separation of monocots and dicots and after the separation of bryophytes and tracheophytes.

Arabidopsis↗
PubMed1990

Structure and expression of the Aplysia californica calmodulin gene.

We have isolated and characterized the calmodulin (CaM) gene of the marine mollusc Aplysia californica. Its primary structure, deduced from the nucleotide sequence of the gene, is highly conserved, containing only three amino acid substitutions compared to the CaM of higher vertebrates. The structural gene consists of four exons that encode the protein, 3' non-translated mRNA and at least one additional exon encoding 5' non-translated mRNA and the initiator methionine. A comparison of the exon/intron structure of CaM genes from several organisms shows conservation of intron position, suggesting that introns have been both inserted and deleted during evolution. Northern analysis of RNA prepared from several Aplysia tissues reveals the presence of several CaM mRNA transcripts with the greatest expression observed in neural and muscle tissue. One of these transcripts is abundant only in mRNA prepared from nervous tissue.

Amino Acid Sequence↗
PubMed1995

Chromosomal assignment and genomic structure of Il15.

Interleukin-15 (IL-15) is a novel cytokine whose effects on T-cell activation and proliferation are similar to those of interleukin-2 (IL-2), presumably because IL-15 utilizes the beta and gamma chains of the IL-2 receptor. Murine IL-15 cDNA and genomic clones were isolated and characterized. The murine Il15 gene was found to consist of eight exons spanning at least 34 kb and was localized to the central region of mouse chromosome 8 by interspecific backcross analysis. Intron positions in a partial human IL15 genomic clone were identical with positions of corresponding introns in the murine gene. The human IL15 gene was mapped to human chromosome 4q31 by fluorescence in situ hybridization.

Amino Acid Sequence↗