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[Statistical characteristics of splicing sites in vertebrates and invertebrates].

Human, rodent, Drosophila and nematode Caernorabditis elegans splicing sites have been analyzed. The estimated strength of the nematode donor sites positively correlates with the length of the adjacent exon. The Drosophila acceptor site strength negatively correlates with the length of the adjacent intron. GC-content of the polypyrimidine tract of the human and rodent acceptor sites and the G/A choice in the third intron position of the human donor sites correlates with the local GC-content of the site neighbourhood.

Animals↗

PubMed1992

Exon-intron organization of the Arabidopsis thaliana protein kinase genes CDC2a and CDC2b.

We have previously shown by cDNA cloning that a higher plant, Arabidopsis thaliana, possesses at least two CDC2 genes (CDC2a and CDC2b) similar to the cell-cycle-controlling cdc2 gene of Schizosaccharomyces pombe. To understand the exon-intron organization of these genes, genomic clones were isolated and their nucleotide sequences determined. The coding and 5'-untranslated regions of CDC2a were interrupted by seven and one introns, respectively, whilst CDC2b contained three introns within the coding portion. These intron positions partly overlapped with each other and with those of the yeast cdc2 gene, nevertheless the lengths and sequences of the corresponding introns were diverse.

Amino Acid Sequence↗

PubMed1996

Arabidopsis thaliana contains two differentially expressed farnesyl-diphosphate synthase genes.

The enzyme farnesyl-diphosphate synthase (FPS; EC 2.5.1.1/EC 2.5.1.10) catalyzes the synthesis of farnesyl diphosphate (FPP) from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This reaction is considered to be a rate-limiting step in isoprenoid biosynthesis. Southern blot analysis indicates that Arabidopsis thaliana contains at least 2 genes (FPS1 and FPS2) encoding FPS. The FPS1 and FPS2 genes have been cloned and characterized. The two genes have a very similar organization with regard to intron positions and exon sizes and share a high level of sequence similarity, not only in the coding region but also in the intronic sequences. Northern blot analysis showed that FPS1 and FPS2 have a different pattern of expression. FPS1 mRNA accumulates preferentially in roots and inflorescences, whereas FPS2 mRNA is predominantly expressed in inflorescences. The cDNA corresponding to the FPS1 gene was isolated by functional complementation of a mutant yeast strain defective in FPS activity (Delourme, D., Lacroute, F., and Karst, F. (1994) Plant Mol. Biol. 26, 1867-1873). By using a reverse transcription-polymerase chain reaction strategy we have cloned the cDNA corresponding to the FPS2 gene. Analysis of the FPS2 cDNA sequence revealed an open reading frame encoding a protein of 342 amino acid residues with a predicted molecular mass of 39,825 Da. FPS1 and FPS2 isoforms share an overall amino acid identity of 90.6%. Arabidopsis FPS2 was able to rescue the lethal phenotype of an ERG20-disrupted yeast strain. We demonstrate that FPS2 catalyzes the two successive condensations of IPP with both DMAPP and geranyl diphosphate leading to FPP. The significance of the occurrence of different FPS isoforms in plants is discussed in the context of the complex organization of the plant isoprenoid pathway.

Alkyl and Aryl Transferases↗

PubMed2001

The cytochrome P450 gene superfamily in Drosophila melanogaster: annotation, intron-exon organization and phylogeny.

The cytochrome P450 gene superfamily is represented by 90 sequences in the Drosophila melanogaster genome. Of these 90 P450 sequences, 83 code for apparently functional genes whereas seven are apparent pseudogenes. More than half of the genes belong to only two families, CYP4 and CYP6. The CYP6 family is insect specific whereas the CYP4 family includes sequences from vertebrates. There are eight genes coding for mitochondrial P450s as deduced from their homology to CYP12A1 from the house fly. The genetic map of the distribution of D. melanogaster P450 genes shows (a) the absence of P450 genes on the chromosome 4 and Y, (b) more than half of the P450 genes are found on chromosome 2, and (c) the largest cluster contains nine genes. Sequence alignments were used to draw phylogenetic trees and to analyze the intron-exon organization of each functional P450 gene. Only five P450 genes are intronless. We found 57 unique intron positions, of which 23 were phase zero, 19 were phase one and 15 were phase two. There was a relatively good correlation between intron conservation and phylogenetic relationship between members of the P450 subfamilies. Although the function of many P450 proteins from vertebrates, fungi, plants and bacteria is known, only a single P450 from D. melanogaster, CYP6A2, has been functionally characterized. Gene organization appears to be a useful tool in the study of the regulation, the physiological role and the function of these P450s.

Alternative Splicing↗

PubMed2003

Polymorphisms in the +252(A/G) lymphotoxin-alpha and the -308(A/G) tumor necrosis factor-alpha genes and susceptibility to chronic periodontitis in a Czech population.

BACKGROUND: Periodontitis is an inflammatory disease that leads to irreversible attachment loss, bone destruction and eventually tooth loss. Tumor necrosis factor (TNF), a pluripotent proinflammatory cytokine that is able to induce tissue destruction and bone resorption, has been implicated in the pathogenesis of periodontal disease. METHODS: In this study, we investigated an association between chronic periodontitis and two previously described bi-allelic polymorphisms in the TNF locus: a G to A transition at position -308 in the 5'promoter region of the TNF-alpha gene and an NcoI restriction fragment length polymorphism (RFLP) in the first intron (position +252A/G) of the lymphotoxin alpha (LT-alpha) gene. Genomic DNA was obtained from 132 patients with chronic periodontitis together with 114 age- and gender-matched unrelated control subjects. RESULTS: The TNF-alpha (-308G/A) polymorphism itself showed no association with chronic periodontitis, whereas the frequency distribution of the LT-alpha (+252A/G) genotypes showed statistically significant differences between patients and the reference group. The proportion of individuals carrying the LT-alpha 1/1 genotype was significantly lower in the group of patients with chronic periodontitis (0.8%) than in the control group (8.8%) (P < 0.0094, Pcorr < 0.05). However, the significant differences in the frequencies of the combined genotypes (TNF-alpha and LT-alpha) between the control and the patient groups were found using a simulation by applying the Monte-Carlo method (P < 0.01). CONCLUSION: Our data suggest that combined genotypes composed of the TNF-alpha and LT-alpha gene polymorphisms may influence the susceptibility to chronic periodontitis. We also showed that, comparing the two genes, the 1/1 genotype of the NcoI polymorphism in the first intron of the LT-alpha gene is a more informative marker and it may be one of the protective genetic factors against chronic periodontitis in our population.

Adenine↗

PubMed1998

The gene encoding the myeloid-related protein 14 (MRP14), a calcium-binding protein expressed in granulocytes and monocytes, contains a potent enhancer element in the first intron.

Myeloid-related proteins 8 and 14 (MRP8 and MRP14) are two Ca2+-binding proteins of the S-100 family highly abundant in myelomonocytic cells. The expression is not only dependent on the developmental status of the cell but also on the inflammatory situation in the tissue. In order to identify regulatory elements responsible for the high expression of MRP14 in myeloid cells, reporter gene constructs have been transfected into HL-60 cells, Mono Mac 6 cells, and L132 cells. We demonstrated that a DNA element in the first intron (positions 153-361) enhances the transcriptional activity of the homologous promoter and of the heterologous herpes simplex virus thymidine kinase promoter up to 37-fold. To further identify the functional site, the region between positions 153 and 192 was analyzed functionally using the thymidine kinase promoter. The region increased the expression in the same magnitude as the complete intron. This enhancer is highly conserved in the human and murine MRP genes, indicative of its involvement in the transcription of MRPs. Protein binding to the region is demonstrated using EMSA, DNA cross-linking, Southwestern blotting, and affinity purification. Affinity purification confirms that four proteins bind to the enhancer element.

Antigens, Differentiation↗

PubMed2001

The beta-tubulin-encoding gene from Microbotryum violaceum: unusual in a variety of ways.

The beta-tubulin gene of Microbotryum violaceum was sought originally for its potential use in improving the transformation of this organism. The gene was cloned and its nucleotide sequence was determined. The gene was predicted to encode a 444-residue protein with strong sequence similarity to other beta-tubulins. The coding region was 2.85 kb, much larger than the corresponding genes from other organisms. This was due to the large number of introns in this gene, as determined by comparison of the cDNA sequence with that for the genomic clone. This gene contained 14 introns, which is the most introns in a beta-tubulin-encoding gene yet reported for any organism. Intron position comparisons between the M. violaceum gene and those from beta-tubulin genes of other organisms revealed a striking result, since 10 of the 14 introns were unique. An additional feature of the gene's organization was an unusually long 5' untranslated region, predicted to be nearly 1 kb in length. The possible significance of these unusual features of genetic structure is discussed.

Amino Acid Sequence↗

PubMed2004

Evolutionary relationships among beta-tubulin gene sequences of basidiomycetous fungi.

36 fungal beta-tubulin sequences were analysed to study the evolution of this gene and the phylogeny of basidiomycetes. The analysis comprises a representative selection of all major lineages of basidiomycetous fungi and some selected ascomycetes for comparison. Intron positions vary between the different lineages, but seem to be conserved in the Hymenomycetes and Ustilaginomycetes. The most conserved regions seem to be highly susceptible for introns. Splicing and branching sites of the introns are more variable in basidiomycetes than reported from other fungal groups so far. Basidiomycete monophyly was confirmed with our data in respect to the ascomycetes studied. By analysing amino acid sequences, the Hymenomycetes and the Ustilaginomycetes were resolved as monophyletic groups. The phylogeny within these two groups is similar to that obtained with other genes. Based on beta-tubulin data Naohidea sebacea, Chionosphaera apobasidialis, Jaculispora submersa, Platygloea pustulata, Platygloea disciformis and Melampsora lini, representing the Urediniomycetes, are not resolved in most analyses. The early radiation of major basidiomycetous lineages seems to be reflected in the highly conserved beta-tubulin gene.

Basidiomycota↗

PubMed2001

Parthenocarpic apple fruit production conferred by transposon insertion mutations in a MADS-box transcription factor.

Fruit development in higher plants normally requires pollination and fertilization to stimulate cell division of specific floral tissues. In some cases, parthenocarpic fruit development proceeds without either pollination or fertilization. Parthenocarpic fruit without seed has higher commercial value than seeded fruit. Several apple (Malus domestica) mutants (Rae Ime, Spencer Seedless and Wellington Bloomless) are known to produce only apetalous flowers that readily go on to develop into parthenocarpic fruit. Through genetics, a single recessive gene has been identified to control this trait in apple. Flower phenotypes of these apple mutants are strikingly similar to those of the Arabidopsis mutant pistillata (pi), which produces flowers where petals are transformed to sepals and stamens to carpels. In this study, we have cloned the apple PI homolog (MdPI) that shows 64% amino acid sequence identity and closely conserved intron positions and mRNA expression patterns to the Arabidopsis PI. We have identified that in the apetalous mutants MdPI has been mutated by a retrotransposon insertion in intron 4 in the case of Rae Ime and in intron 6 in the case of Spencer Seedless and Wellington Bloomless. The insertion apparently abolishes the normal expression of the MdPI gene. We conclude that the loss of function mutation in the MdPI MADS-box transcription factor confers parthenocarpic fruit development in these apple varieties and demonstrates another function for the MADS- box gene family. The knowledge generated here could be used to produce parthenocarpic fruit cultivars through genetic engineering.

Amino Acid Sequence↗

PubMed2026

Long-read transcriptomics corrects Trichomonas vaginalis intron annotations and refines transcript-end features.

BACKGROUND: Trichomonas vaginalis causes the most prevalent non-viral sexually transmitted infection worldwide. Despite its large genome (181.5 Mb; 36,310 predicted protein-coding genes in NYU_TvagG3_2), intron annotations remain limited and inconsistently validated. A recent short-read RNA-seq study reported 63 putative active introns, but short reads can misassign splice boundaries and cannot resolve complete transcript structures. METHODS: We integrated Oxford Nanopore direct RNA sequencing (DRS), ONT cDNA long-read sequencing, and Illumina RNA-seq to refine intron annotations, transcript-end features, and UTR boundaries in T. vaginalis. Candidate introns were validated by targeted PCR and Sanger sequencing, and representative splicing events were further assessed using public SRA datasets. RESULTS: Starting from 31 historically annotated introns, motif-guided long-read screening and orthogonal validation identified 17 additional validated introns, increasing the curated set to 48 confirmed introns. Among these 17 events, three were previously unrecognized in the current NYU_TvagG3_2 reference annotation. We also corrected five reported loci, including two false-positive introns, two splice-coordinate misannotations, and one gene-sequence error. DRS further supported transcript termination site mapping, UAAA polyadenylation-signal profiling relative to poly(A) addition sites, and single-molecule poly(A)-tail estimation. StringTie mixed-mode assemblies provided updated UTR boundaries for intron-bearing transcripts and transcripts without curated introns. CONCLUSIONS: This study provides a rigorously validated, long-read-refined resource of intron annotations, UTR boundaries, and UAAA-guided transcript-end features for T. vaginalis, together with a reproducible workflow for non-model protists. These refinements improve the current reference annotation and support future studies of functional genomics, parasite biology, pathogenesis, and diagnostic development.

Trichomonas vaginalis↗

PubMed1988

Structural organization of the mouse cytosolic malate dehydrogenase gene: comparison with that of the mouse mitochondrial malate dehydrogenase gene.

We cloned and characterized a mouse cytosolic malate dehydrogenase (cMDHase) (EC 1.1.1.37) gene, which is about 14 x 10(3) base-pairs long and is interrupted by eight introns. The 5' and 3' flanking regions and the exact sizes and boundaries of the exon blocks, including the transcription-initiation sites, were determined. The 5' end of the gene lacks the TATA and CAAT boxes characteristic of eukaryotic promoters, but contains G + C-rich sequences, one putative binding site for a cellular transcription factor, Sp1, and at least two major transcription-initiation sites. The sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. We compared structural organization of the mouse cMDHase gene with that of the previously characterized mouse mitochondrial MDHase (mMDHase) gene, and found that the conservation of intron positions spreads across much of the two genes. This result suggests that a common ancestral gene for the cytosolic MDHase and the mitochondrial MDHase was broken up by introns, before the divergence. We also compared the nucleotide sequence of the promoter region of the mouse cytosolic MDHase gene with that of the other three mouse genes coding for isoenzymes participating in the malate-aspartate shuttle, i.e. mitochondrial MDHase, cytosolic and mitochondrial aspartate aminotransferases (cAspATase and mAspATase). We found that highly conserved regions are present in the promoter region of the cAspATase gene.

Amino Acid Sequence↗

PubMed1986

A canonical sequence organization at the 5'-end of the myosin heavy chain genes.

The sequences encoding the 5'-ends of three chicken fast-white myosin heavy chain (MHC) genes have been determined. When compared with the sequences of two other MHC genes it is apparent that both the exon and intron positions are conserved. All exon sequences are highly conserved; there is absolute amino acid conservation in the second and third exons. In addition, while the first and third introns diverge among the genes, the second intron is highly conserved between the five. This intron contains a 24-bp sequence that is repeated twice in one of the introns and once in the other four. Analyses indicate that this sequence, which is partially homologous to 7SL RNA, appears to be largely restricted to the MHC gene family. Analysis of the 5'-flanking sequences show that while small homologies are present between some of the genes, they have extensively diverged in this region.

Amino Acid Sequence↗

PubMed1992

Structure and evolution of the human prosaposin chromosomal gene.

The gene for prosaposin was characterized by sequence analysis of chromosomal DNA to gain insight into the evolution of this locus that encodes four highly conserved sphingolipid activator proteins or saposins. The 13 exons ranged in size from 57 to 1200 bp, while the introns were from 91 to 3812 bp in length. The regions encoding saposins A, B, and D each had three exons, while that for saposin C had only two. This sequence included the regions that encode the carboxy terminus of the signal peptide, the four mature prosaposin proteins, and the 3' untranslated region. Primer extension studies indicated that over 99% of the coding sequence was contained in these 19,985 bp. Use of PCR and reverse PCR techniques indicated that the most 5' coding approximately 140 bp contained large introns and at least two small exons. Analyses of the intronic positions in the saposin regions indicated that this gene evolved from an ancestral gene by two duplication events and at least one gene rearrangement involving a double crossover after introns had been inserted into the gene.

Animals↗

PubMed1997

The gene of the neural cell recognition molecule F11: conserved exon-intron arrangement in genes of neural members of the immunoglobulin superfamily.

The chicken neural glycoprotein F11 is a cell recognition molecule implicated in neurohistogenesis, in particular in the context of neurite outgrowth and fasciculation. F11 is a glycosyl-phosphatidylinositol-linked member of the immunoglobulin superfamily that is also termed contactin or F3 in humans and rodents, respectively. In this study, we report the complete structure of the F11 gene. It is composed of 23 exons distributed over more than 100 kb of genomic DNA and each of the ten domains of the F11 protein is encoded by two exons. The sizes of the introns vary by two orders of magnitude ranging from 150 bp to more than 15 kb. All interdomain introns are in phase one, i.e. are inserted after the first nucleotide of a codon, being consistent with assembly of a F11 progenitor gene via exon shuffling. The intradomain introns are localized at variable sites within the domains and have different intron phases. This study reveals a remarkable similarity of the F11 gene with the gene of axonin-1, a related neural immunoglobulin superfamily member which is also implicated in neurite outgrowth and fasciculation. The intron positions with respect to the protein domain organization are found to be identical, strongly suggesting that both genes are derived from a common ancestor that already had this exon-intron structure.

Animals↗

PubMed2004

IGF2 antisense transcript expression in porcine postnatal muscle is affected by a quantitative trait nucleotide in intron 3.

A paternally expressed quantitative trait locus (QTL) for muscle mass was mapped to the insulin-like growth factor II (IGF2) locus at the distal end of pig chromosome 2p. It was recently demonstrated that a G to A transition at position intron 3-nt 3072 is the quantitative trait nucleotide (QTN) underlying this QTL. In this study we report for the first time the existence of imprinted porcine IGF2 antisense transcripts (IGF2-AS) and demonstrate that their expression in postnatal muscle is also affected by the QTN. A coregulated expression of IGF2 and IGF2-AS RNAs in muscle and liver with decreasing transcription from fetal to adult age was demonstrated. Further, the significant difference found in expression of IGF2-AS in postnatal muscle between individuals with different QTL genotypes and the lack of significant differences in fetal muscle and liver reflect completely what has been found for IGF2 sense transcripts.

Animals↗

PubMed1998

Genomic organization of four beta-1,4-endoglucanase genes in plant-parasitic cyst nematodes and its evolutionary implications.

The genomic organization of genes encoding beta-1,4-endoglucanases (cellulases) from the plant-parasitic cyst nematodes Heterodera glycines and Globodera rostochiensis (HG-eng1, Hg-eng2, GR-eng1, and GR-eng2) was investigated. HG-eng1 and GR-eng1 both contained eight introns and structural domains of 2151 and 2492bp, respectively. HG-eng2 and GR-eng2 both contained seven introns and structural domains of 2324 and 2388bp, respectively. No significant similarity in intron sequence or size was observed between HG-eng1 and HG-eng2, whereas the opposite was true between GR-eng1 and GR-eng2. Intron positions among all four cyst nematode cellulase genes were conserved identically in relation to the predicted amino acid sequence. HG-eng1, GR-eng1, and GR-eng2 had several introns demarcated by 5'-GCellipsisAG-3' in the splice sites, and all four nematode cellulase genes had the polyadenylation and cleavage signal sequence 5'-GAUAAA-3'-both rare occurences in eukaryotic genes. The 5'- flanking regions of each nematode cellulase gene, however, had signature sequences typical of eukaryotic promoter regions, including a TATA box, bHLH-type binding sites, and putative silencer, repressor, and enhancer elements. Database searches and subsequent phylogenetic comparison of the catalytic domain of the nematode cellulases placed the nematode genes in one group, with Family 5, subfamily 2, glycosyl hydrolases from Scotobacteria and Bacilliaceae as the most homologous groups. The overall amino acid sequence identity among the four nematode cellulases was from 71 to 83%, and the amino acid sequence identity to bacterial Family 5 cellulases ranged from 33 to 44%. The eukaryotic organization of the four cyst nematode cellulases suggests that they share a common ancestor, and their strong homology to prokaryotic glycosyl hydrolases may be indicative of an ancient horizontal gene transfer.

3' Untranslated Regions↗

PubMed1993

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins.

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.

Animals↗

PubMed1993

The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

The ges-1 gene codes for a non-specific carboxylesterase that is normally expressed only in the intestine of the nematode Caenorhabditis elegans. In the current paper, we describe the cloning and characterization of the ges-1 gene from C. elegans, as well as the homologous gene from the nematode Caenorhabditis briggsae. The ges-1 esterases from the two nematodes are 83% identical at the amino acid level and contain regions of significant similarity to insect and mammalian esterases; these conserved regions can be identified with residues believed to be necessary for esterase function. The ges-1 mRNAs from both C. elegans and C. briggsae are trans-spliced. The coding regions, the codon bias and the splicing signals of the two ges-1 genes are quite similar and most (6/7) of the intron positions are retained precisely. Yet, the flanking sequences of the two ges-1 genes appear to have diverged almost completely. For example, the C. elegans ges-1 5'-flanking region (as well as several introns) contains copies of three different SINE-like sequences, previously identified near the hsp-16 genes, near the unc-22 gene and in a repetitive element CeRep-3; none of these elements are found in the C. briggsae ges-1 gene. We show that: (1) the C. elegans ges-1 gene can be used to transform C. briggsae, whereupon expression of the exogenous ges-1 gene is confined to the C. briggsae intestine; (2) the ges-1 homologue cloned from C. briggsae can be transformed into C. elegans, whereupon it is expressed largely in the C. elegans intestine; and (3) a 5'-deletion of the C. elegans ges-1 gene that we have previously shown to be expressed in the C. elegans pharynx is also expressed in the pharynx of C. briggsae (either in the presence or absence of vector sequences). These results suggest that the ges-1 gene control circuits have been maintained between the two nematode species, despite the divergent 5'-flanking sequences of the gene. This raises the question of the evolutionary distance between C. elegans and C. briggsae and we attempt to estimate the C. elegans-C. briggsae divergence time by analysing the rate of synonymous substitutions in coding regions of ges-1 and six other C. elegans-C. briggsae gene pairs. We propose a new method of analysis, which attempts to remove rate differences found between different genes by extrapolating to zero codon bias.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗