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PubMed1998

Group I introns found in Chlorella viruses: biological implications.

More than 80 group I introns were detected and characterized in Chlorella viruses isolated from various locations in Japan; the overall average frequency of viruses containing the group I intron was 8.0%. Although most of these introns were inserted in the gene for either transcriptional elongation factor TFIIS (approximately 60%) or URF 14.2 (unidentified open reading frame coding for a 14.2-kDa polypeptide) (approximately 40%), in a few cases, the gene for the major capsid protein Vp52 contained an intron. These introns were biologically active (self-splicing) both in vivo and in vitro. Viruses that contained introns almost usually contained only one, but more than two introns coexisted in several virus isolates. Nucleotide sequence analysis showed that the intron sequences have diverged under strong constraint of the exon genes: introns in the same gene showed more than 99% sequence identity, whereas introns in different genes were only 72-78% identical. Phylogenetic analysis suggested relatedness of these introns to those found in the rRNA genes of a variety of organisms including green algae, red algae, red algae, yeasts, fungi, and protozoa.

Base Sequence↗

PubMed1999

Evolution of Mhc-DRB introns: implications for the origin of primates.

Introns are generally believed to evolve too rapidly and too erratically to be of much use in phylogenetic reconstructions. Few phylogenetically informative intron sequences are available, however, to ascertain the validity of this supposition. In the present study the supposition was tested on the example of the mammalian class II major histocompatibility complex (Mhc) genes of the DRB family. Since the Mhc genes evolve under balancing selection and are believed to recombine or rearrange frequently, the evolution of their introns could be expected to be particularly rapid and subject to scrambling. Sequences of intron 4 and 5 DRB genes were obtained from polymerase chain reaction-amplified fragments of genomic DNA from representatives of six eutherian orders-Primates, Scandentia, Chiroptera, Dermoptera, Lagomorpha, and Insectivora. Although short stretches of the introns have indeed proved to be unalignable, the bulk of the intron sequences from all six orders, spanning >85 million years (my) of evolution, could be aligned and used in a study of the tempo and mode of intron evolution. The analysis has revealed the Mhc introns to evolve at a rate similar to that of other genes and of synonymous sites of non-Mhc genes. No evidence of homogenization or large-scale scrambling of the intron sequences could be found. The Mhc introns apparently evolve largely by point mutations and insertions/deletions. The phylogenetic signals contained in the intron sequences could be used to identify Scandentia as the sister group of Primates, to support the existence of the Archonta superorder, and to confirm the monophyly of the Chiroptera.

Animals↗

PubMed2002

Dynamic insertion-deletion of introns in deuterostome EF-1alpha genes.

To test the validity of intron-exon structure as a phylogenetic marker, the intron-exon structure of EF-1alpha genes was investigated for starfish, acornworms, ascidians, larvaceans, and amphioxus and compared with that of vertebrates. Of the 11 distinct intron insertion sites found within the coding regions of the deuterostome EF-1alpha genes, 7 are shared by several taxa, while the remainder are unique to certain taxa. Examination of the shared introns of the deuterostome EF-1alpha gene revealed that independent intron loss or intron insertion must have occurred in separate lineages of the deuterostome taxa. Maximum parsimony analysis of the intron-exon data matrix recovered five parsimonious trees (consistency index = 0.867). From this result, we concluded that the intron-exon structure of deuterostome EF-1alpha has evolved more dynamically than previously thought, rendering it unsuitable as a phylogenetic marker. We also reconstructed an evolutionary history of intron insertion-deletion events on the deuterostome phylogeny, based on several molecular phylogenetic studies. These analyses revealed that the deuterostome EF-1alpha gene has lost individual introns more frequently than all introns simultaneously.

Amino Acid Sequence↗

PubMed2006

Tempo and mode of spliceosomal intron evolution in actin of foraminifera.

Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago.

Actins↗

PubMed2006

A gradient in the distribution of introns in eukaryotic genes.

The majority of eukaryotic genes consist of exons and introns. Introns can be inserted either between codons (phase 0) or within codons, after the first nucleotide (phase 1) and after the second (phase 2). We report here that the frequency of phase 0 increases and phase 1 declines from the 5' region to the 3' end of genes. This trend is particularly noticeable in genomes of Homo sapiens and Arabidopsis thaliana, in which gains of novel introns in the 3' portion of genes were probably a dominant process. Similar but more moderate gradients exist in Drosophila melanogaster and Caenorhabditis elegans genomes, where the accumulation of novel introns was not a prevailing factor. There are nine types of exons, three symmetric (0,0; 1,1; 2,2) and six asymmetric (0,1; 1,0; 1,2; 2,1; 2,0; 0,2). Assuming random distribution of different types of introns along genes, one can expect the frequencies of asymmetric exons such as 0,1 and 1,0 or 1,2 and 2,1 to be approximately equal, allowing for some variation caused by randomness. The gradient in intron distribution leads to a small but consistent and statistically significant bias: phase 1 introns are more likely at the 5' ends and phase 0 introns are more likely at the 3' ends of asymmetric exons. For the same reason, the frequency of 0,0 exons increases and the frequency of 1,1 exons decreases in the 3' direction, at least in H. sapiens and A. thaliana. The number of introns per gene also affects the distribution and frequency of phase 0 and 1 introns. The gradient provides an insight into the evolution of intron-exon structures of eukaryotic genes.

Animals↗

PubMed2007

Patterns of group I intron presence in nuclear SSU rDNA of the Lichen family Parmeliaceae.

Group I introns are commonly reported within nuclear SSU ribosomal DNA of eukaryotic micro-organisms, especially in lichen-forming fungi. We have studied the primary and secondary structure of 70 new nuclear SSU rDNA group I introns of Parmeliaceae (Ascomycota: Lecanorales) and compared them with those available in databases, covering more than 60 species. The analyzed samples of Parmeliaceae fell into two groups, one having an intron at the 1506 site and another lacking this one but having another at the 1516 or 1521 position. Introns at the 1521 position seem to be transposed from 1516 sites. Introns at the 1516 position were similar in structure to ones previously reported at this site and known from other lecanoralean fungi, while those at the 1506 position showed structural differences and no similar introns are known from related fungi. The study of the distribution of group I introns within a large monophyletic ensemble of fungi has revealed an unexpected correlation between intron types and ecological and geographical parameters. The introns at the 1516 position occurred in mainly arctic, boreal, and temperate lichens, while those at position 1506 were present in mainly tropical and subtropical to oceanic mild-temperate taxa. Further, the 1516 introns occurred in genera with few distributed species that could represent older taxa, while the 1506 ones were mainly in species-rich genera that could be of recent speciation, as many species have wide distribution areas. The transition between two different environments has been accompanied by a change in introns gained and lost.

Amino Acid Sequence↗

PubMed2000

Intron conservation in a UV-specific DNA repair gene encoded by chlorella viruses.

Large dsDNA-containing chlorella viruses encode a pyrimidine dimer-specific glycosylase (PDG) that initiates repair of UV-induced pyrimidine dimers. The PDG enzyme is a homologue of the bacteriophage T4-encoded endonuclease V. The pdg gene was cloned and sequenced from 42 chlorella viruses isolated over a 12-year period from diverse geographic regions. Surprisingly, the pdg gene from 15 of these 42 viruses contain a 98-nucleotide intron that is 100% conserved among the viruses and another 4 viruses contain an 81-nucleotide intron, in the same position, that is nearly 100% identical (one virus differed by one base). In contrast, the nucleotides in the pdg coding regions (exons) from the intron-containing viruses are 84 to 100% identical. The introns in the pdg gene have 5'-AG/GTATGT and 3'-TTGCAG/AA splice site sequences which are characteristic of nuclear-located, spliceosomal processed pre-mRNA introns. The 100% identity of the 98-nucleotide intron sequence in the 15 viruses and the near-perfect identity of an 81-nucleotide intron sequence in another 4 viruses imply strong selective pressure to maintain the DNA sequence of the intron when it is in the pdg gene. However, the ability of intron-plus and intron-minus viruses to repair UV-damaged DNA in the dark was nearly identical. These findings contradict the widely accepted dogma that intron sequences are more variable than exon sequences.

Amino Acid Sequence↗

PubMed1996

Identification of a group I intron in the nuclear small subunit rDNA of Pseudohalonectria lignicola.

A 865-bp insertion was detected within the nuclear small subunit (SSU) rDNA in two isolates (intron+) of the freshwater ascomycete Pseudohalonectria lignicola by the polymerase chain reaction (PCR). The intron sequences from the two isolates were identical to each other, and the exon sequences from the two intron+ isolates were identical to those in the intron- isolates in the PCR-amplified region of rDNA. Reverse transcription PCR (RT-PCR) indicated that the intron was absent in the mature rRNA. The intron sequence has all the characteristics of a group I intron, including four conserved sequence elements (P, Q, R, and S), the presence of a U at the 5' splice site of the exon, a G at the 3' splice site of the intron, a putative internal guiding sequence, and the sequence fit a secondary structure model for group I introns. Like most introns found in nuclear rDNA, this intron was located at a highly conserved region and was devoid of long open reading frames.

Ascomycota↗

PubMed2000

A group I intron in the nuclear small subunit ribosomal DNA of Gaeumannomyces graminis.

The length of the small subunit ribosomal DNA (SSU rDNA) differs among isolates of species and varieties of Gaeumannomyces. The sequence of the 3' region of the SSU rDNA revealed 340-, 365-, and 520-bp insertions for G. graminis varieties avenae, tritici, and graminis, respectively. The intron sequences from varities tritici and avenae were similar, except there was an insert of 23 nucleotides at base 328 from the 5' end of the G. g. var. tritici intron. The G. g. var. graminis intron sequences had 92.4% homology compared with the intron sequences of varieties tritici and avenae. In addition, the intron sequence of variety graminis is larger, having an insert of 155 nucleotides at base 365 of the 5' end of the intron. Little variation in the DNA sequences flanking the introns has been detected among the isolates of Gaeumannomyces that either have or lack an intron. Reverse transcriptase PCR (RT-PCR) indicated the absence of the intron in the mature rRNA. The intron sequence had both a conserved sequence and secondary structural elements classifying it as a group I intron.

Ascomycota↗

PubMed1999

The catalytic group-I introns of the psbA gene of chlamydomonas reinhardtii : core structures, ORFs and evolutionary implications.

The sequences and predicted secondary structures of the four catalytic group-I introns in the psbA gene of Chlamydomonas reinhardtii, Cr.psbA-1-Cr.psbA-4, have been determined. Cr.psbA-1 and Cr.psbA-4 are subgroup-IA1 introns and have similar secondary structures, except at the 3' end where Cr.psbA-1 contains a large inverted-repeat domain. Cr.psbA-4 is closely related to intron 1 of the Chlamydomonas moewusii psbA gene, with which it shares the same location, high nucleotide identity in the core, and an identically placed ORF that shows 58% amino-acid identity. Cr.psbA-2 is a subgroup-IA3 intron, and shows similarities to the Chlamydomonas eugametos rRNA intron, Ce.LSU-1. Cr.psbA-3 is a subgroup-IA2 intron, and is remarkably similar to the T4 phage intron, sunY. Interestingly, a degenerate version of Cr.psbA-3 is located in the intergenic region between the chloroplast petA and petD genes. All four introns contain ORFs, which potentially code for basic proteins of 11-38 kDa. The ORFs in introns 2 and 3 contain variants of the GIY-YIG motif; however, the Cr.psbA-2 ORF is free-standing, whereas the Cr.psbA-3 ORF is contiguous and in-frame with the upstream exon. The Cr.psbA-4 ORF contains an H-N-H motif, and possibly a GIY-YIG motif. These data indicate that the C. reinhardtiipsbA introns have multiple origins, and illustrate some of the evolutionary DNA dynamics associated with group-I introns in Chlamydomonas.

Algal Proteins↗

PubMed2001

Variation in sequence and RNA editing within core domains of mitochondrial group II introns among plants.

The 3' regions of several group II introns within the mitochondrial genes nad1 and nad7 show unexpected sequence divergence among flowering plants, and the core domains 5 and 6 are predicted to have weaker helical structure than those in self-splicing group II introns. To assess whether RNA editing improves helical stability by the conversion of A-C mispairs to A-U pairs, we sequenced RT-PCR amplification products derived from excised intron RNAs or partially spliced precursors. Only in some cases was editing observed to strengthen the predicted helices. Moreover, the editing status within nad1 intron 1 and nad7 intron 4 was seen to differ among plant species, so that homologous intron sequences shared lower similarity at the RNA level than at the DNA level. Plant-specific variation was also seen in the length of the linker joining domains 5 and 6 of nad7 intron 3; it ranged from 4 nt in wheat to 11 nt in soybean, in contrast to the 2-4 nt length typical of classical group II introns. However, this intron is excised as a lariat structure with a domain 6 branchpoint adenosine. Our observations suggest that the core structures and sequences of these plant mitochondrial introns are subject to less stringent evolutionary constraints than conventional group II introns.

Alternative Splicing↗

PubMed1997

Extensive structural conservation exists among several homologs of two Euglena chloroplast group II introns.

82 of the 155 chloroplast introns in Euglena gracilis have been categorized as group II introns. Because they are shorter and more divergent than group II introns from other organisms, the assignment of these Euglena introns to the group II class has been questioned. In the current study, two homologs of E. gracilis petB intron 1 and four homologs of psbC intron 2 have been isolated from related species and characterized. Based on a comparative sequence analysis of intron homologs, the intron core and four of the six helical domains present in the canonical group II intron structural model are conserved in E. gracilis petB intron 1 and psbC intron 2 and all of their homologs. Distal portions of domain I, which are involved in most of the tertiary interactions, are less well conserved than the central core.

Animals↗

PubMed2004

Two self-splicing group I introns interrupt two late transcribed genes of prolate-headed Lactobacillus delbrueckii phage JCL1032.

Two group I introns were detected from the late gene region of the prolate-headed phage JCL1032 of Lactobacillus delbrueckii. Introns JCL-I1 and JCL-I2 interrupt orf602 and orf1868 encoding a phage terminase large subunit (TerL, 69.7 kDa) and a putative tape measure protein (TMP, 202 kDa), respectively. The introns JCL-I1 (226 bp) and JCL-I2 (322 bp) were efficiently self-spliced in vivo. Both introns were classified to the subgroup IA1 having all the conserved structures necessary for splicing, but lacking the ability to encode endonucleases or other gene products. The introns JCL-I1 and JCL-I2 shared restricted nucleotide sequence similarity with each other and with the group I terL intron of Lb. delbrueckii phage LL-H. No match was found for JCL-I1 in the homology searches. Instead, the primary sequence from the joining region of P8 and P7 to P9 of the intron JCL-I2 was homologous to the group I intron of Bacillus mojavensis; the orf142 introns I1, I2 and I3 of Staphylococcus aureus phage Twort; the group I intron of phage Bastille (Bacillus thuringiensis); and to the group IA3 intron of Monomastix species.

Amino Acid Sequence↗

PubMed2006

Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor.

Group II introns are widespread in plant cell organelles. In vivo, most if not all plant group II introns do not self-splice but require the assistance of proteinaceous splicing factors. In some cases, a splicing factor (also referred to as maturase) is encoded within the intronic sequence and produced by translation of the (excised) intron RNA. However, most present-day group II introns in plant organellar genomes do not contain open reading frames (ORFs) for splicing factors, and their excision may depend on proteins encoded by other organellar introns or splicing factors encoded in the nuclear genome. Whether or not the ancestors of all of these noncoding organellar introns originally contained ORFs for maturases is currently unknown. Here we show that a noncoding intron in the mitochondrial cox2 gene of seed plants is likely to be derived from an ancestral reverse transcriptase/maturase-encoding form. We detected remnants of maturase and reverse transcriptase sequences in the 2.7 kb cox2 intron of Ginkgo biloba, the only living species of an ancient gymnosperm lineage, suggesting that the intron originally harbored a splicing factor. This finding supports the earlier proposed hypothesis that the ancient group II introns that invaded organellar genomes were autonomous genetic entities in that they encoded the factor(s) required for their own excision and mobility.

Amino Acid Sequence↗

PubMed1987

Structural organization of the 5' region of the thyroglobulin gene. Evidence for intron loss and "exonization" during evolution.

More than one third of thyroglobulin (1190 residues out of 2750) is made of one peptide motif repeated ten times in tandem. Segments unrelated to the motif interrupt this structure at various places. The corresponding gene region, which extends over 40 x 10(3) bases, was studied in detail. All exon borders and exon/intron junctions were localized precisely and sequenced, and their positions were correlated with the repetitive organization of the protein. When intron positions were compiled on a consensus sequence of all repeats, three categories of introns were observed. Except between repeats numbers 5 and 6, an intron was invariably found within the Cys codon making the limit of each motif. This category of intron most probably reflects the serial duplication events responsible for the evolution of this region of the gene. All other introns, except no. 2, are found at positions were the repetitive structure is disrupted by "inserted" peptides. We present the hypothesis that this second category of introns was already present in the original unit before the first duplication. Thereafter, they would have experienced either complete loss (some units do not contain any intron) or partial or total exonization, resulting in the slipping of intronic material into coding sequence. Intron no. 2, finally, separates motif no. 1 at a position on the boundary between two segments presenting sequence homology. This last type of intron probably reflects an initial duplication event at the origin of a primordial thyroglobulin gene motif. With all these characteristics, the thyroglobulin gene is presented as a paradigm for the analysis of the fate of introns in gene evolution.

Amino Acid Sequence↗

PubMed1995

Comparison of introns in a cdc2-homologous gene within a number of Plasmodium species.

The first three introns of CRK2, a cdc2-homologous gene, have been compared in a total of seven Plasmodium species. The introns were located at conserved sites, suggesting an ancestral origin. Interspecific comparison of intron sequences agreed with the previously inferred evolutionary relationships of the malaria parasites. Unlike the introns in the rodent malaria species, the similarity of the CRK2 introns was regionalized between the human parasite P. vivax and the simian parasite P. knowlesi: the central region of all three introns showed markedly less interspecific similarity than the 5' and 3' regions. This was also in contrast with the organisation and composition of homologous intron pairs from other genes of the same two species. No conservation at the level of secondary structure could be detected, even between highly similar introns. A database search for intron-containing Plasmodium genes was performed. All introns obtained in this way plus the additional CRK2 introns were scanned for the presence of putative branching site consensus sequences. For P. falciparum, we present an update of the 5' and 3' splice-site consensus.

Amino Acid Sequence↗

PubMed1989

Introns in the 3'-untranslated region can inhibit chimeric CAT and beta-galactosidase gene expression.

The expression of a cyc::cat [cytochrome c/chloramphenicol acetyltransferase (CAT)] chimeric gene was stimulated 100-fold by the inclusion of a cyc intron in the 5'-untranslated region. In contrast, a single intron in the 3'-untranslated region was at best only slightly stimulatory, and surprisingly, inhibited expression of cat when an intron was also included in the 5'-untranslated region. This inhibition was independent of the identity of the downstream intron, occurring when either the simian virus 40 (SV40) small t intron or a cyc intron was located downstream from the cat coding region. Analysis of CAT mRNA levels, using a riboprobe spanning the 5' end of the CAT message, revealed that the stimulatory effect of a 5'-noncoding region intron were manifest at both the protein and RNA levels, whereas the inhibitory effects of 3'-noncoding region introns were detectable only at the protein level. The effects of intron position on chimeric gene expression were observed in both primate and rodent cell lines and also when the beta-galactosidase coding region was substituted for that of cat. Therefore, the common placement of an intron in the 3'-noncoding region is not the most beneficial to the expression of cyc chimeric genes. The position of introns within a transcriptional unit is a major factor to be considered when optimizing the efficiency of animal cell expression vectors.

Animals↗

PubMed1993

On the ancient nature of introns.

We discuss some of the arguments for introns arising early or late in evolution. We outline the exon theory of genes and discuss the series of discoveries of introns in the gene (TPI) encoding triosephosphate isomerase (TPI) that have filled out a series of better fits to the Go plot, culminating in the 1986 prediction of an intron position that was finally discovered in 1992. We present a statistical argument that the 11-intron structure of TPI (based on attributing all of the introns to an ancestral gene and interpreting three cases of very close intron positions as examples of sliding) has a clear relationship to the protein structure. The exons of this 11-intron TPI are a better approximation to Mitiko Go's modules (Go, 1981) than are 99.9% of all alternative exon patterns corresponding to 11 introns placed randomly in the gene, and better than 96% of all alternative patterns in which the lengths of the exons are preserved while the introns are moved. We combine four tests relating exons to protein structure: (i) whether the exons are compact modules, (ii) whether the exons contain most of the close contacts in the protein, (iii) whether the exon configuration maximized buried surface area along the backbone, and (iv) whether the exons maximize their content of hydrogen bonds. On a joint measure for these tests, the native exon structure with 11 introns fits these tests better than 99.4% of all alternative structures obtained by permuting the exon lengths and intron positions.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗