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PubMed2006

Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics.

Nuclear DNA intron sequences are increasingly used to investigate evolutionary relationships among closely related organisms. The phylogenetic usefulness of intron sequences at higher taxonomic levels has, however, not been firmly established and very few studies have used these markers to address evolutionary questions above the family level. In addition, the mechanisms driving intron evolution are not well understood. We compared DNA sequence data derived from three presumably independently segregating introns (THY, PRKC I and MGF) across 158 mammalian species. All currently recognized extant eutherian mammalian orders were included with the exception of Cingulata, Dermoptera and Scandentia. The total aligned length of the data was 6366 base pairs (bp); after the exclusion of autapomorphic insertions, 1511 bp were analyzed. In many instances the Bayesian and parsimony analyses were complementary and gave significant posterior probability and bootstrap support (>80) for the monophyly of Afrotheria, Euarchontoglires, Laurasiatheria and Boreoeutheria. Apart from finding congruent support when using these methods, the intron data also provided several indels longer than 3 bp that support, among others, the monophyly of Afrotheria, Paenungulata, Ferae and Boreoeutheria. A quantitative analysis of insertions and deletions suggested that there was a 75% bias towards deletions. The average insertion size in the mammalian data set was 16.49 bp +/- 57.70 while the average deletion was much smaller (4.47 bp +/- 14.17). The tendency towards large insertions and small deletions is highlighted by the observation that out of a total of 17 indels larger than 100 bp, 15 were insertions. The majority of indels (>60% of all events) were 1 or 2 bp changes. Although the average overall indel substitution rate of 0.00559 per site is comparable to that previously reported for rodents and primates, individual analyses among different evolutionary lineages provide evidence for differences in the formation rate of indels among the different mammalian groups.

Animals↗
PubMed2003

The first intron of the murine beta-casein gene contains a functional promoter.

Caseins are the major milk proteins in most mammals. Together with calcium and phosphate they form the casein micelle. The corresponding casein genes are clustered in mammalian genomes and their expression is coordinately regulated with regard to developmental and tissue specificity. Casein gene promoters are responsive to lactogenic hormones, cell-matrix, and cell-cell interactions. Transcriptional enhancer elements are found in the 5(') upstream regions of casein genes but have also been detected in the first intron of the bovine beta-casein gene. We show here that the first intron of the murine beta-casein gene has three discernible functions. First, transcriptional enhancer elements present in the intron increase the basal activity of the beta-casein promoter. In addition, these intronic enhancer elements augment the induction of the beta-casein promoter by lactogenic hormones. Finally, we demonstrate that the first intron of the murine beta-casein gene contains a functional promoter.

Animals↗
PubMed1997

Essential role of the first intron in the transcription of hsp90beta gene.

The human HSP90 gene family contains introns. There are two typical heat shock elements (HSE) in the first intron of human hsp90beta gene. As detected by chloramphenicol acetyl transferase (CAT) reporter activity assays, the HSE-containing intron is essential in maintaining high constitutive expression and is critical for heat shock inducibility of the human hsp90beta gene. Cellular heat shock factor 1 (HSF 1) shows much higher binding affinity toward the intronic HSEs in comparison to an atypical HSE in the 5' flanking sequence. Novel initiation sites found in the first intron probably also contribute to constitutive and heat-inducible expression of the hsp90beta gene in Jurkat cells.

Chloramphenicol O-Acetyltransferase↗
PubMed2003

Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease.

A large number of group I introns encode a family of homologous proteins that either promote intron splicing (maturases) or are site-specific DNA endonucleases that function in intron mobility (a process called "homing"). Genetic studies have shown that some of these proteins have both activities, yet how a single protein carries out both functions remains obscure. The similarity between respective DNA-binding sites and the RNA structure near the 5' and 3' splice sites has fueled speculation that such proteins may use analogous interactions to perform both functions. The Aspergillus nidulans mitochondrial COB group I intron encodes a bi-functional protein, I-AniI, that has both RNA maturase and site-specific DNA endonuclease activities in vitro. Here, we show that I-AniI shows distinctive features of the endonuclease family to which it belongs, including highly specific, tight binding and sequential DNA strand cleavage. Competition experiments demonstrate that I-AniI binds the COB intron RNA even in saturating concentrations of its DNA target site substrate, suggesting that the protein has a separate binding site for RNA. In addition, we provide evidence that two different DNA-binding site mutants of I-AniI have little effect on the protein's RNA maturation activity. Since RNA splicing is likely a secondary adaptation of the protein, these observations support a model in which homing endonucleases may have developed maturase function by utilizing a hitherto "non-functional" protein surface.

Amino Acid Substitution↗
PubMed1996

The DExH box protein Suv3p is a component of a yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity.

The yeast mitochondrial protein Suv3p is a putative NTP-dependent RNA helicase. Here we report that in cells lacking Suv3p, there is an approximately 50-fold increase in the excised form of the group I intron omega of the mitochondrial 31S rRNA gene. Surprisingly, little mature 21S rRNA accumulates in those cells; instead, unligated 21S rRNA exons appear. Intron overaccumulation could lead to spliced exon reopening via a reaction known to be catalyzed by group I introns in vitro. We also show that Suv3p is a functional component of a novel mitochondrial NTP-dependent 3'-to-5' exoribonuclease activity that can degrade group I intron RNAs. These findings account for group I intron overaccumulation in cells lacking Suv3p and define a novel function for putative RNA helicases in direct RNA degradation.

Base Sequence↗
PubMed1988

Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desulfurococcus mobilis.

The intron of the 23S rRNA gene of D. mobilis is excised from the pre-23S RNA at specific sites in vivo and subsequently ligated to form a stable circular RNA, with a normal 5'-3' phosphodiester bond, containing the entire intron sequence; 95% of this RNA codes for a protein of 194 amino acids that can be expressed in E. coli. Crude cell extracts from D. mobilis also induce a two-step slicing reaction in vitro, producing the same circular intron RNA but a low yield of ligated exons. Cleavage depends on the RNA structure adjacent to the cleavage site and yields a 3'-terminal phosphate. Splicing is enhanced by GTP, but does not require divalent metal ions. The cleavage and exon-splicing reactions resemble those found for tRNA introns in eukaryotes and a possible structural rationale for this similarity is considered together with its possible implications for the origin of eukaryotic rRNA and tRNA introns.

Amino Acid Sequence↗
PubMed2000

Transcriptional regulation involving the intronic heat shock element of the rat hsp27 gene.

While sequencing the first intron of the rat heat shock protein 27 gene (hsp27), we identified a consensus heat shock regulatory element (HSE). This intronic HSE (i-HSE) is conserved among mammalian hsp27 genes. The aim of this study was to investigate possible effects of this intronic HSE (i-HSE) on transcription from the rat hsp27 promoter. Gel mobility shift assays indicated that the i-HSE bound heat shock transcription factor 1 (HSF1) in a manner equivalent to that of HSE present in hsp27 promoter (p-HSE). The effect of i-HSE on transcription from the hsp27 promoter was evaluated using reporter constructs transiently transfected in the osteosarcoma cell line ROS17/2.8. When inserted 5' to a 145 bp fragment of the hsp27 promoter not containing p-HSE, a 215 bp fragment of hsp27 intron 1 containing i-HSE enhanced CAT activity and conferred heat shock-inducible activity to the construct. This intronic fragment containing i-HSE also enhanced CAT activity in either normal or heat-shocked culture conditions when inserted 3' to the CAT open reading frame. However, in chimeric reporter constructs with a 273 bp hsp27 promoter containing p-HSE directly 5' to CAT reporter, and with a 215 bp fragment containing i-HSE inserted 3' to the CAT open reading frame, transcription from hsp27 promoter was reduced under normal and heat-stressed culture conditions. Mutation of the i-HSE reversed this effect. Further study is required to define the mechanism by which the i-HSE-containing region of the hsp27 promoter may mediate negative regulation of hsp27 transcription.

Animals↗
PubMed2001

Leaving group stabilization by metal ion coordination and hydrogen bond donation is an evolutionarily conserved feature of group I introns.

To understand the behavior of group I introns on a biologically fundamental level, we must distinguish those traits that arise as the products of natural selection (selected traits) from those that arise as the products of neutral drift (non-selected traits). In practice, this distinction relies on comparing the similarities and differences among widely divergent introns to identify conserved traits. Here we address whether the strategies used by the eukaryotic group I intron from the Tetrahymena ciliate to stabilize the leaving group during splicing are maintained in the group I intron from the widely divergent Azoarcus bacterium. A substrate analogue containing a 3'-phosphorothiolate linkage, in which a sulfur atom replaces the bridging 3'-oxygen atom of the scissile phosphate, reacts 20-fold slower in the Azoarcus reaction than the corresponding unmodified substrate in the presence of Mg(II) as the only divalent cation. However, Mn(II) relieves this negative effect such that the 3'-S-P bond cleaves 21-fold faster than does the 3'O-P bond. Other thiophilic divalent metal ions such as Co(II), Cd(II), and Zn(II) similarly support cleavage of the S-P bond. These results indicate that a metal ion directly coordinates to the leaving group in the transition state of the Azoarcus ribozyme reaction. Additionally, the 3'-sulfur substitution eliminates the approximately 10(3)-fold contribution of the adjacent 2'-OH to transition state stabilization. Considering that sulfur accepts hydrogen bonds weakly compared to oxygen, this result suggests that the 2'-OH contributes to catalysis by donating a hydrogen bond to the 3'-oxygen leaving group in the transition state, presumably acting in conjunction with the metal ion to stabilize the developing negative charge. These same catalytic strategies of metal ion coordination and hydrogen bond donation operate in the Tetrahymena ribozyme reaction, suggesting that these features of catalysis have been conserved during evolution and thus extend to all group I introns. The two ribozymes also exhibit quantitative differences in their response to 3'-sulfur substitution. The Azoarcus ribozyme binds and cleaves the phosphorothiolate substrate more efficiently relative to the natural substrate than the Tetrahymena ribozyme under the same conditions, suggesting that the Azoarcus ribozyme better accommodates the phosphorothiolate at the active site both in the ground state and in the transition state. These differences may reflect either a less tightly knit Azoarcus structure and/or spatial deviations between backbone atoms in the two ribozymes that arise during divergent evolution, analogous to the well-documented relationship between protein sequence and structure.

Animals↗
PubMed1999

Promoter and exon-intron structure of the protein kinase C gene from the marine sponge Geodia cydonium: evolutionary considerations and promoter activity.

We report the gene structure of a key signaling molecule from a marine sponge, Geodia cydonium. The selected gene, which codes for a classical protein kinase C (cPKC), comprises 13 exons and 12 introns; the introns are, in contrast to those found in cPKC from higher Metazoa, small in size ranging from 93 nt to 359 nt. The complete gene has a length of 4229 nt and contains exons which encode the characteristic putative regulatory and catalytic domains of metazoan cPKCs. While in the regulatory domain only one intron is in phase 0, in the catalytic domain most introns are phase 0 introns, suggesting that the latter only rarely undergo module duplication. The 5'-flanking sequence of the sponge cPKC gene contains a TATA-box like motif which is located 35-26 nt upstream from the start of the longest sequenced cDNA. This 5'-flanking sequence was analyzed for promoter activity. The longest fragment (538 nt) was able to drive the expression of luciferase in transient transfections of NIH 3T3 fibroblasts; the strong activity of the sponge promoter was found to be half the one displayed by the SV40 reference promoter. Deletion analysis demonstrates that the AP4 site and the GC box which is most adjacent to the TATA box are the crucial elements for maximal promoter activity. The activity of the promoter is not changed in 3T3 cells which are kept serum starved or in the presence of a phorbol ester. In conclusion, these data present the phylogenetically oldest cPKC gene which contains in the 5'-flanking region a promoter functional in the heterologous mammalian cell system.

3T3 Cells↗
PubMed1996

Site-specific substitution of inosine at the terminal positions of a pre-mRNA intron: implications for the configuration of the terminal base interaction.

Genetic evidence in yeast has revealed that a non-Watson-Crick base-pairing interaction between terminal guanosine residues of the intron is required for the second step of pre-mRNA splicing. To explore the likely configuration of the interaction between the terminal guanosines of the intron, inosine was uniformly incorporated into an adenovirus pre-mRNA substrate (Ade) to replace guanosine residues. Splicing of the inosine-containing Ade pre-mRNA was completely inhibited. Psoralen cross-linking reveals that the association of U1 and U2 snRNPs with the intron was impaired. To eliminate the deleterious effects caused by complete inosine replacement, guanosine residues at the splice site(s) of the Ade pre-mRNA were substituted by inosine. Such pre-mRNA substrates were obtained by ligation of two or three RNA fragments; the 3' piece was primed with inosine or mono-phosphate inosine. Splicing of the Ade pre-mRNA containing an inosine residue at the 5' or the 3' splice site, or at both sites proceeds normally. Thus, the functions of the terminal guanosine residues of the intron in splicing can be replaced by inosine. This result supports the previous notion that an N1-carbonyl symmetric interaction likely occurs between the intron terminal residues during pre-mRNA splicing.

Base Composition↗
PubMed2003

The 4830C>A polymorphism within intron 5 affects the pattern of alternative splicing occurring within exon 6 of the thrombopoietin gene.

OBJECTIVE: A common variant in intron 5 of the thrombopoietin (TPO) gene (4830C>A) has been associated with risk of myocardial infarction (MI). To explore the molecular mechanism of this association, the ability of the intron to act as a transcription enhancer and to influence mRNA splicing was tested. METHOD AND RESULTS: In HepG2 cells the presence of intron 5 upstream of the TPO promoter decreased promoter activity to between 60% and 30%. This effect was orientation dependent; in the reverse orientation, intron 5 caused a twofold greater decrease in promoter activity compared to the forward orientation. However, the effects were similar with either the C or the 4830A allele. An in vitro exon trapping system was used to study the effect of the polymorphism on splicing events in exon 6. The full-length (TPO-1) and three previously reported splice variants (TPO-2, TPO-3, and TPO-5) were identified. The 4830A allele resulted in a small but statistically significant increase in production of the TPO-3 splice variant relative to the full-length transcript (10.6%+/-0.6%) compared to the 4830C allele (8.3%+/-0.6%) (p=0.02). Generation of TPO-5 was also slightly increased, but this did not reach significance. CONCLUSION: The identification of a potential "silencer" sequence in intron 5 of the TPO gene demonstrates the complexity of control of expression of the gene. Although the precise role of the different splice variants is not known, the finding that the 4830C>A sequence change alters their relative amounts, suggests a possible molecular mechanism whereby TPO genotype may influence the risk of MI.

Alternative Splicing↗
PubMed2002

Intron-mediated expression of the human neuropeptide Y Y1 receptor.

The Neuropeptide Y (NPY) family of neuropeptides exert their function through a family of heptahelical G-protein coupled receptors regulating essential physiological processes. A 97 base pair intron (intron IV) intervenes the coding sequence of the human NPY Y1 receptor (hY1) gene and was found frequently retained at variable levels in poly A+ mRNA isolated from multiple human tissues. When included in hY1 expression vectors, either in its natural position or 5' of the hY1 cDNA, intron IV mediated a significant increase of both hY1 mRNA and corresponding functional receptor protein in transfected mammalian cells, implying an in vivo regulatory function of the endogenous intron. Our results further indicate that the nuclear history of the hY1 pre-mRNA influence ectopic hY1 production through post-transcriptional mechanisms and argues against intron IV acting as a transcriptional enhancer as well as the possibility that a putative hY1 related 5TM accessory protein encoded by the non-spliced hY1 mRNA would facilitate hY1 production on a post-translational level.

5' Untranslated Regions↗
PubMed1997

A genomic element within the third intron of the human oxytocin receptor gene may be involved in transcriptional suppression.

The human oxytocin receptor (OTR) gene comprises a large (> 10 kb) third intron between the regions encoding the transmembrane domains six and seven. It has been shown for other genes that transcriptional control elements may reside within such introns, and that these may correlate with changes in the methylation status of the DNA. Methylation mapping indeed indicated that within this third intron there was a region which appeared to be hypermethylated in non-expressing tissues, but relatively hypomethylated in the myometrium of the cycle and at term, when the OTR gene is upregulated. We then employed in vitro nuclear protein-DNA binding assays to evaluate the importance of this region in the control of the human OTR gene. As source of nuclear proteins we have compared a non-expressing tissue, human peripheral blood leucocytes, with human myometrium from the cycle (low expression) and from term pregnancy (high expression). It could be shown that a specific motif of ca. 10-15 nucleotides close to the middle of the third intron specifically binds nuclear proteins correlating with the down-regulated state of the gene. The accumulated data suggest that this intronic element is specifically binding nuclear protein(s) associated with a suppression of OTR gene activity.

Base Sequence↗
PubMed2001

Two-domain hemoglobin gene of the water flea Moina macrocopa: duplication in the ancestral Cladocera, diversification, and loss of a bridge intron.

Two cDNAs encoding the two-domain hemoglobin (Hb) chains of a crustacean Cladocera, Moina macrocopa, were cloned and their nucleotide (nt) sequences were determined. The amino acid (aa) sequences of both the gene products deduced from the nt sequences consisted of 348 residues and showed 98% identity with each other. These sequences together with the NH(2)-terminal aa sequences of the Hb chains determined after separation by two-dimensional gel electrophoresis showed that the Hb chains are synthesized as a secretory precursor with a signal peptide of 17 aa residues. The aa sequences of M. macrocopa Hb chains shared the following features with those of Daphnia Hb chains. Firstly, the signal peptide is followed by an NH(2)-terminal extension containing a threonine-rich sequence that might play a role in the multimerization of subunit chains. Secondly, the identity between the aa sequences of the first and second domains is exceptionally low. These facts suggest that duplication of the cladoceran Hb gene occurred before the divergence of families Moinidae and Daphniidae. Analysis of genomic DNA showed that the M. macrocopa Hb genes consist of two large repeated regions, encoding the first and second domains of Hb chains, respectively. The intron-exon organization of the first region of the M. macrocopa Hb genes was similar to that found in the Daphnia Hb genes, having the three-exon, two-intron structure characteristic of animal Hb genes. However, the intron bridging the two regions and the most downstream intron in the second region were missing in the Moina genes, providing a new example of intron loss. The following elements in the 5' flanking region were conserved in the Moina and Daphnia genes: (1) TATAAA, a typical TATA box sequence accompanied by a downstream sequence, GAAXAGCATCAGTT (the fourth residue X was G or A in Daphnia and absent in Moina); (2) CCAAT boxes, located upstream of the TATA box; (3) the binding sites for HIF-1 and GATA-1, also located upstream of the TATA box, that may be responsible for up-regulation of the cladoceran Hb genes under hypoxia.

Amino Acid Sequence↗
PubMed2002

Identification and characterization of bacterial class E group II introns.

Group II introns are catalytic RNAs and mobile genetic elements. Phylogenetic characterization of group II intron-encoded reverse transcriptases (RTs) established seven classes: the mitochondrial class, chloroplast-like classes 1 and 2, and bacterial classes A, B, C, and D. In this study, we identified and characterized a new bacterial class of group II introns, bacterial class E, on the basis of phylogenetic analysis of the intron-encoded protein (IEP) RT and determination of a consensus intron RNA structure.

Bacteria↗
PubMed2003

An inserted DNA fragment with plasmid features is uniquely associated with the presence of the GBSi1 group II intron in Streptococcus agalactiae.

The group II intron (GBSi1) identified downstream of the C5a-peptidase gene (scpB) in a subpopulation of Streptococcus agalactiae isolates is a suggested marker for a separate genetic lineage of serotype III isolates. In the present study two additional copies of GBSi1, one of which not previously described, were identified among serotype III isolates. All intron copies shared a common target site motif. A single copy of GBSi1 was found in a subgroup of serotype II and V isolates. In these isolates, the intron had inserted downstream of scpB, which suggests that this is the primary insertion site for GBSi1. Most bacterial group II introns described to date reside in transposable elements. The scpB locus was found to be flanked by insertion sequences similar to what has been described in an intronless serotype Ia isolate. However, this region contained an additional 2.1 kb DNA fragment present only in intron carrying isolates. This DNA fragment contained a partial transposase and putative plasmid related proteins. This may suggest that GBSi1 once was brought into the S. agalactiae genome by an integrated plasmid.

Base Sequence↗
PubMed1996

Detection and characterization of two novel hypervariable microsatellite repeat regions within intron 2 of the alpha-globin gene of the bivalve mollusc Anadara trapezia.

Synthetic oligonucleotide primers based on cDNA sequence were used to amplify the region spanning intron 2 of the alpha-globin gene of the bivalve mollusc Anadara trapezia. Amplification of this region from individual clams showed highly polymorphic patterns. The sequence of this intron was found to include a number of mono- [d(T)n and d(C)n], di- [d(CA)n and d(CT)n] and tetranucleotide d(CTGT)n repeats which were found to be polymorphic with respect to the types and numbers of repeats present. Two separate repeat-containing polymorphic regions were located near each end of this intron. The repeat at the 3' end consisted of an unusual example of a d(T)n polymorphism at the position of the polypyrimidine tract usually involved in intron splicing. Thirteen individual cloned intron 2 sequences, derived by PCR amplification from pooled genomic DNA, were sequenced without finding two identical sequences. All of the sequenced clones contained microsatellite sequences.

Animals↗
PubMed1997

The correlation between introns and the three-dimensional structure of proteins.

We test the hypothesis that introns were used to construct the first genes from small exons, whose protein products represent compact elements of structure. For any three-dimensional structure, a computer program analyzes the structure into a set of modules, segments of the polypeptide chain bounded in space by a maximum diameter, separated by a set of 'boundary regions'. The 'boundary regions' are such that if the gene were divided by an intron in each 'boundary region', the protein would be divided into modules less than the specified diameter. Using a set of 32 ancient proteins, which have no introns in prokaryotes, we examine the intron positions in their eukaryotic homologs and show that the introns are correlated with modules of diameter 21, 28 and 33 A, with P values below 0.001.

Exons↗