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At least 1,279 records · Page 71Linked to original sources
PubMed1993

Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria.

Group II introns al1 and al2 of the yeast mtDNA cox1 gene encode reverse transcriptase-like proteins that function in RNA splicing and may play a role in intron mobility and excision. We find that ribonucleoprotein particles from yeast mitochondria contain a reverse transcriptase activity that is likely encoded by al1 and al2 and is highly specific for the introns and their flanking exons. Using a mutant strain with elevated activity, we show that the reverse transcriptase uses either excised intron RNA or cox1 pre-mRNA as template and initiates cDNA synthesis near the 3' end of al2 and immediately downstream in E3. Our results suggest that introns al1 and al2 are retroelements, which encode reverse transcriptases that have adapted to function in RNA splicing.

Base Sequence↗
PubMed1995

Group II intron mobility occurs by target DNA-primed reverse transcription.

Mobile group II introns encode reverse transcriptases and insert site specifically into intronless alleles (homing). Here, in vitro experiments show that homing of the yeast mtDNA group II intron aI2 occurs by reverse transcription at a double-strand break in the recipient DNA. A site-specific endonuclease cleaves the antisense strand of recipient DNA at position +10 of exon 3 and the sense strand at the intron insertion site. Reverse transcription of aI2-containing pre-mRNA is primed by the antisense strand cleaved in exon 3 and results in cotransfer of the intron and flanking exon sequences. Remarkably, the DNA endonuclease that initiates homing requires both the aI2 reverse transcriptase protein and aI2 RNA. Parallels in their reverse transcription mechanisms raise the possibility that mobile group II introns were ancestors of nuclear non-long terminal repeat retrotransposons and telomerases.

Base Sequence↗
PubMed1989

Bacteriophage introns: parasites within parasites?

Several bacteriophage introns carry the information necessary to perform a complex series of RNA as well as DNA rearrangements. The RNA splicing reactions allow expression of the intron-containing genes, whereas recombination at the DNA level results in the mobility and invasive potential of the introns. The RNA and DNA transactions are temporally regulated to permit timely splicing early in infection, and expression of intron-encoded DNA endonucleases involved in mobility at late times. This is achieved through efficient use of the viral regulatory machinery, ensuring the perpetuation of the 'parasitic' introns.

Animals↗
PubMed1996

Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron.

Like most mitochondrial group I introns with a free-standing open reading frame (ORF) located downstream of their catalytic core, the Sd.cob, 1 intron in the gene coding for the cytochrome b of Saccharomyces douglasii mitochondria possesses a putative proximal 3' splice site. However, incubation of Sd.cob, 1 preRNA transcripts under optimal in vitro splicing conditions essentially results in splicing at the authentic, distal 3' splice junction. The mechanism by which the proximal splicing event is suppressed in vitro involves formation of a tertiary interaction which is only found in the Sd.cob, 1 intron. Core nucleotides located in loop L5 block proximal splicing by forming Watson-Crick base pairs with the nucleotide sequence of the proximal 3' splice site. This tertiary base pairing, also important for the folding of the intron into an active conformation, may be regarded as equivalent to the L9/P5, GNRA-loop/helix interaction found in more than one-third of known group I introns.

Alternative Splicing↗
PubMed1989

The catalytic core of the sunY intron of bacteriophage T4.

The self-splicing sunY intron of bacteriophage T4 shares a common secondary structure with other group I introns. A long open reading frame within the intron is entirely 3' of the structural elements conserved in all group I introns. This catalytic core is the smallest yet described for a self-splicing intron. An internal deletion of 728 nucleotides (nt), leaving 196 nt at the 5' end and 109 nt at the 3' end, allows normal self-splicing. Transcripts terminating 196 nt 3' of the 5' splice site retain catalytic activity.

Catalysis↗
PubMed1995

Comparison of repetitive elements in the third intron of human and rodent mitochondrial benzodiazepine receptor-encoding genes.

The third intron of the mitochondrial benzodiazepine receptor (MBR)-encoding gene was sequenced from hamster, mouse and human. The rodent species were found to include an Alu-like sequence, as was first discovered in the rat gene. Differences with the rat intron were evident by an insertion of an additional B1 element in the hamster and the introduction of a complete and two partial B2 sequences in the mouse intron. The human intron contained a cluster of four Alu sequences; however, all of these repetitive elements were found to be in the opposite orientation relative to the Alu-like sequence present in the rodent genes. These findings support the possibility that the rodent Alu-like sequence is a remnant of a retropositional insertion in this gene prior to the divergence of rodent species. Because the human intron does not contain the same Alu remnant, it cannot be concluded that the rodent sequence represents an insertion of a primordial Alu element prior to the divergence of rodent and primate lineages.

Animals↗
PubMed1995

A calcineurin-B-encoding gene expressed during differentiation of the amoeboflagellate Naegleria gruberi contains two introns.

One of two similar genes in the unicellular eukaryote Naegleria gruberi is shown to encode calcineurin B (CnB), the regulatory subunit of calcium-calmodulin-regulated protein phosphatase 2B. Over a span of 156 amino acids, excluding divergent N-termini, the encoded sequence shows 62% identity with vertebrate CnB, and also shows sequence elements specific, among calcium-binding proteins, to CnB. In contrast, the sequence shows only 23% identity with N. gruberi flagellar calmodulin. CNB mRNA is readily detected in amoebae; its abundance increases fourfold during differentiation to flagellates, reaches a peak at 50-70 min, when flagella are forming, and then declines. A genomic clone matches an expressed cDNA, except that it is interrupted by two phase I introns. The position of one intron, which separates the divergent N-terminal domain from the four calcium-binding domains (EF hands), is shared with a yeast CNB gene; the other is located in the central helix between the two pairs of calcium-binding loops; features that support an ancient origin. These introns, the first found in protein-coding genes of Naegleria, are flanked by characteristic splice junction sequences. N. gruberi CnB also shares similarities with recoverins. The finding in a protist of a CNB gene that contains two introns separating functional domains, shares similarities to recoverins and shows increased expression during differentiation is provocative. If the phylogeny of major groups derived from ribosomal RNA is accepted, Naegleria is among the earliest branching eukaryotes known to contain canonical pre-mRNA introns.

Amino Acid Sequence↗
PubMed1994

Deletion of P9 and stem-loop structures downstream from the catalytic core affects both 5' and 3' splicing activities in a group-I intron.

The P9 stem-loop is one of the conserved structural elements found in all group-I introns. Using two deletion mutants in this region of the Tetrahymena thermophilia large ribosomal subunit intron, we show that removal of the P9 element, either alone, or together with the non-conserved downstream P9.1 and P9.2 elements, results in an intron incapable of the first step of the splicing reaction at a low concentration of Mg2+. The mutant introns also require high concentrations of Mg2+ for the second step in splicing, as well as hydrolysis reactions, suggesting that P9, as well as P9.1 and P9.2, are important structural elements in the final folded form of the intron. In addition, RNase-T1-mediated-structure-probing experiments demonstrated that the loss of P9, P9.1 and P9.2 changes the structural context of the region binding the 5' splice site. The deletions lead to less efficient recognition of the 3' splice site and an accumulation of unligated exons. These observations support the view that the P9, P9.1 and P9.2 stem-loops play an important role in the binding of the 3' splice site.

Animals↗
PubMed1996

A group II intron in a conjugative transposon from the gram-positive bacterium, Clostridium difficile.

We have been studying the conjugative transposon Tn5397, originally isolated from the Gram-positive pathogen Clostridium difficile. Physical analysis of this transposon demonstrated that it contained a group II intron. This is the first report of an intron in a conjugative transposon and the first report of a group II intron in Gram-positive bacteria. The intron interrupted a gene in Tn5397 that is almost identical to orf14 from Tn916. DNA hybridisation analysis showed that elements related to Tn5397, containing the group II intron, were present in five other C. difficile strains from different geographical locations suggesting that the element is likely to be widely distributed.

Cloning, Molecular↗
PubMed1992

Did the ancestral globin gene of plants and animals contain only two introns?

All vertebrate globin genes contain two introns, while plant globin genes contain three. It is widely thought that the plant gene structure reflects the structure of the primordial globin gene and that a common ancestor of all animals lost the central intron shortly after the divergence of plants and animals more than one billion years ago. The recent discovery of a discordant central intron in some animal globin genes suggests that this model is incorrect. We propose that the typical vertebrate two-intron gene structure is the primordial eukaryotic form, and that following the divergence of plants and animals, a common ancestor of plants gained a central intron in the globin gene.

Amino Acid Sequence↗
PubMed2005

Intronic enhancement of angiotensin II type 2 receptor transgene expression in vitro and in vivo.

The angiotensin II type 2 receptor (AT2R) can influence a variety of intracellular signaling molecules and cellular functions. However, its physiological functions and the roles of introns in the regulation of its expression have not been well determined. We first demonstrated that both intron 1 and intron 2 of AT2R could significantly enhance AT2R overexpression. Thus, we have provided some new prerequisites for further studies on the mechanisms that control AT2R gene expression. Next, we established a highly efficient method of delivering this receptor in vitro and in vivo using an AT2R recombinant adenoviral vector containing two introns of the AT2R. The vector may be useful in helping to uncover AT2R physiological functions and also for gene therapy related to AT2R. Moreover, we determined the important role of introns in gene expression cassettes and the inconsistency of expression between the targeted gene and the reporter gene.

Angiotensin II↗
PubMed2005

Pushing back the expansion of introns in animal genomes.

In a recent paper in Science, surveyed the position of introns in 30 genes of a marine annelid and showed that over 60% of the introns occupy positions identical to those in human homologs. In contrast, both human and marine annelid genes share only 30% of their introns with other invertebrates. These observations suggest that the common ancestor of most animal phyla had intron-rich genes and reinforce the notion that introns proliferated early in the evolutionary history of eukaryotes.

Animals↗
PubMed2004

Associations of polymorphisms of the angiotensinogen M235 polymorphism and angiotensin-converting-enzyme intron 16 insertion/deletion polymorphism with preeclampsia in Korean women.

OBJECTIVE: The contribution of genetic factors to preeclampsia has been well documented. However, there has not been any study done on the association between preeclampsia and the angiotensinogen (AGT) M235T polymorphism and angiotensin-converting-enzyme (ACE) intron 16 insertion/deletion (I/D) polymorphism among Korean preeclampsia women. We performed a hospital-based case-control study on Korean women to investigate the association between preeclampsia and the angiotensinogen M235T polymorphism and also to determine the association between preeclampsia and the angiotensin-converting-enzyme intron 16 polymorphism. METHODS: DNA was extracted from whole blood of 104 preeclampsia patients and 114 healthy pregnant women. All samples were genotyped for all the polymorphisms using amplification after PCR of known allelic variants. Results were analyzed with the chi-square test, Student's t-test, and logistic regression. RESULTS: 18 of 50 women with preeclampsia (36.0%) in nulliparous women and 15 of 37 women with preeclampsia (40.5%) in parous women were homozygous for methionine (M235) to threonine (T235) substitution at residue 235 of AGT gene, versus 12 of 38 women in nulliparous control women and 18 of 50 women in parous control women. There was no association between the AGT M235T polymorphism and preeclampsia according to age. Fourteen of 55 women with preeclampsia (25.5%) in nulliparous women and 11 of 39 women with preeclampsia (28.2%) in parous women were homozygous for the D allele of the ACE intron 16, versus 9 of 52 women in nulliparous control women and 16 of 53 women in parous control women. No association was demonstrated between D allele of ACE intron 16 and preeclampsia according to age. There were significant differences in birth weight and delivery weeks between controls and preeclampsia patients (P < 0.001). There were no significant differences in age and nulliparity between controls and preeclampsia patients. CONCLUSION: The result indicates that the AGT M235T polymorphism and the ACE intron 16 polymorphism play no significant role in preeclampsia observed in Korean women.

Adult↗
PubMed2005

Housekeeping recA gene interrupted by group II intron in the thermophilic Geobacillus kaustophilus.

Most of group II introns are found in intergenes and CDSs with unknown functions, but not in housekeeping genes. In particular, no group II intron within the housekeeping recA gene has been reported either in eukaryotic genomes or in prokaryotic genomes. In this study, we found that the recA gene of the thermophilic Geobacillus kaustophilus genome is interrupted by a group II intron (Gk. Int1), and that Gk.Int1 can splice in temperatures above 70 degrees C in vivo. Here, we report the first prokaryotic group II intron to be found in a housekeeping gene, the characteristics of its self-splicing in vivo and in vitro, and our conclusion that the recA gene functions through the self-splicing of Gk.Int1. It is suggested that the amelioration of Gk.Int1 intron has occurred recently, and that it is still in the process of evolution to the recipient genome.

Amino Acid Sequence↗
PubMed2005

A study of lipoprotein lipase gene intron 8 polymorphisms in Chinese Han race essential hypertension patients.

OBJECTIVE: To investigate the association of lipoprotein lipase gene intron 8 polymorphisms and Essential Hypertension in Han race Chinese. METHODS AND RESULTS: 116 patients with Essential Hypertension were enrolled and another 116 normal people were served as controls. All cases were examined for the genotypes of intron 8 in lipoprotein lipase gene by the methods of polymerase chain reaction restriction fragment length polymorphism, and the serum lipoprotein levels were also observed. Results showed that body mass index blood pressure and the serum triglyceride level were obviously increased in the Essential Hypertension group. The genotype and allele frequency of intron 8 in lipoprotein lipase in the Essential Hypertension group showed obvious differences compared with the control group. Serum triglyceride levels were higher in the patients with H+H+ genotype than in those in non H+H+ genotype of intron 8 in lipoprotein lipase by HindIII digestion. The systolic blood pressure showed a decreasing tendency among the H+H+ genotype, the H+H- genotype and the H-H- genotype individuals. CONCLUSION: The results suggest that lipoprotein lipase may be an important genetic factor associated with the Chinese Han race Essential Hypertension patients. The polymorphisms of intron 8 in lipoprotein lipase influence the blood-lipid metabolism, induce blood vessel rebuilding and play an important role in the invasion and development of Essential Hypertension.

Asian People↗
PubMed2004

INTROnSPECTIVE and NORA: computerized compositional characterization of regions within introns and around start codons on the basis of non-randomness analysis.

Non-randomness analysis has recently proven a valuable method in the characterization of chromosomes and genomes with respect to the nucleotides around start codons. This methodology has been implemented in a distributable program NORA, which is presented as freeware for users in academia. Moreover, because the current knowledge about introns is limited, another application, INTROnSPECTIVE, has been developed. This application analyzes introns in either direction (from 5' to 3' or from 3' to 5') and the user has the option to exclude introns on the basis of their size or intron number within the gene. Both programs are based on initial parsing of GenBank flatfiles, i.e., with these programs, entire genomes or chromosomes can be parsed and characterized within seconds. The programs run under 32-bit Windows operating systems and can be obtained via . They are the only ones available which perform non-randomness analysis, and INTROnSPECTIVE represents a comprehensive and novel methodology for the study of introns.

Algorithms↗
PubMed2005

Intron 1 of the interferon gamma gene: Its role in nematode resistance in Suffolk and Texel sheep breeds.

Genetic variation at intron 1 of the interferon gamma gene has recently been associated with variation in faecal egg count in Romney, Merino and Soay breeds of sheep. The Texel breed is more resistant to gastrointestinal nematode infection than the Suffolk breed, based on faecal egg count. Hence, the objective of this experiment was to characterise the polymorphisms of intron 1 of the interferon gammagene in Suffolk and Texel sheep, and to determine if the characterised haplotype variants were associated with faecal egg count variation in these breeds. Intron 1 haplotypes and faecal egg measurements were determined for Suffolks (n=113) and Texels (n=135). Four haplotypes were identified in Suffolks (A, B, C and D), two haplotypes as previously described, and two previously unknown haplotypes. However, there was no association between interferon gamma intron 1 haplotype and faecal egg count in Suffolks. In contrast, two previously identified haplotypes (A and B) were present in the Texel breed, and the B haplotype was associated with resistance to nematode infection (P=0.02). These results suggest that intron 1 of the interferon gamma gene has an important role in resistance to nematode infection in the Texel breed.

Animals↗
PubMed2005

Molecular evolution of the trnL(UAA) intron in bryophytes.

Structure, variability, and molecular evolution of the trnL(UAA) intron in bryophytes (mosses and liverworts) is analyzed based on more than 1000 sequences representing all classes, including comparisons of lengths and GC-contents, sequence similarities, evolutionary rates and ti/tv ratios of the major lineages and selected genera. Secondary structure analyses of the more variable stem-loop regions facilitated recognition of sequence repeats and minute inversions that often occurred independently in non-related lineages, thus supporting alignment construction and homology assessment. The most length-variable stem-loop region P8 does not share a common evolutionary history across all major bryophyte lineages. Independent nucleotide additions such as internally repeated sequence segments resulted in non-homologous P8 sequences that cannot be folded into a common P8 secondary structure, neither for all bryophytes nor for liverworts or mosses. To address evolutionary patterns, separate analyses of P6/P8 and the remaining intron (core) have to be performed, as overall values of the complete intron are misleading. It is argued that a transition bias observed above the genus level in the core structure is caused by structural constraints, not by its higher GC-content in comparison to the more AT-rich P6 and P8. Compensating base pair changes detected in highly conserved elements are often characteristic of the major bryophyte lineages (classes). Sequence divergence and evolutionary rates are generally higher in liverworts than in mosses, resulting in ambiguous alignments of P6 and P8 even within classes. In mosses, trends towards length reduction of P8 and lower evolutionary rates of the intron are observed. Average intraspecific variation is less than 1%, corresponding to 2-3 mutations in the complete intron.

Base Composition↗