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Vasku, A., M. Goldbergova, L. Spinarova, J. Spinar, J. Vitovec, and J. Vacha. "TWO INTRONE RXR ALPHA POLYMORPHISMS IN CHRONIC HEART FAILURE." Journal of Hypertension 22, Suppl. 2 (June 2004): S212. http://dx.doi.org/10.1097/00004872-200406002-00739.
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Pavkova Goldbergova, Monika, Lenka Spinarova, Jindrich Spinar, Jiri Vítovec, Jiri Parenica, Martin Poloczek, and Anna Vasku. "RXRA introne polymorphism and ABO blood groups in chronic heart failure." Open Life Sciences 5, no. 6 (December 1, 2010): 749–56. http://dx.doi.org/10.2478/s11535-010-0089-y.
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AbstractRetinoic X receptor alpha (RXRA), a member of nuclear receptor superfamily, plays a key role in development, metabolism, glucose homeostasis, and intestinal cholesterol balance. The aim of this study was to examine an association of RXR alpha introne 5 A(39526)AA polymorphism and ABO blood groups with chronic heart failure (CHF) in the Czech population. A total of 238 patients with chronic heart failure and a control group of 246 subjects were included in the study. The RXR alpha gene polymorphism and ABO blood groups were detected by PCR and RFLP methods. Significant differences in distributions of RXRA A(39526)AA alleles and genotypes between CHF patients and controls were observed (Pg=0.03, Pa=0.02). The RXRA gene polymorphism differences of within blood group A between CHF patients and controls were highly significant in genotype distributions (Pg=0.002) and in allele frequency comparisons (Pa=0.0001). The prevalence of AA allele in CHF patients with A blood group was four-fold lower than in controls with the same blood group (OR=0.24; Pcorr=0.0001). A highly significant association of RXRA introne single-nucleotide insertion polymorphism and A blood group in chronic heart failure was observed. Our results suggest close linkage between RXRA A(39526)AA polymorphism and ABO blood groups.
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Goldbergova, M., I. Spinarova, J. Spinar, J. Vitovec, J. Vacha, and A. Vasku. "INTRONE RXR ALPHA POLYMORPHISM AND A BLOOD GROUP IN CHRONIC HEART FAILURE." Journal of Hypertension 22, Suppl. 2 (June 2004): S345. http://dx.doi.org/10.1097/00004872-200406002-01205.
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Roslim, Dewi Indriyani. "cDNA Actin Isolated From Pandanus Sp." International Journal of Ecophysiology 1, no. 2 (August 31, 2019): 94–100. http://dx.doi.org/10.32734/ijoep.v1i2.1271.
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Actin is one of the reference genes that is often used as an internal control in gene expression analysis. This study aimed to isolate actin cDNA from Pandanus sp originated from Riau. Fresh leaves Pandanus sp. Lake Kajuik, Langgam District, Pelalawan Regency, Riau Province. Isolation of RNA, synthesis of total cDNA, amplification of actin genes used McDowell's designed degenerate primer (PlAc46S-20/PlAc245N-20), electrophoresis, sequencing, and data analysis. Actin cDNA fragments obtained were 353 pb in size, registered at GenBank and encoded 117 amino acids. Actin cDNA fragment consists of two exons and one introne. Specific actin primers from Riau Pandanus sp. can be designed based on sequences obtained for the purpose of analyzing certain gene expressions.
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Zhu, D. F., Z. H. Hu, and J. M. Shen. "Moult-Inhibiting Hormone from the Swimming Crab, Portunus Trituberculatus (Miers, 1876): PCR Cloning, Tissue Distribution, and Expression of Recombinant Protein in Escherichia Coli (Migula, 1895)." Crustaceana 84, no. 12-13 (2011): 1481–96. http://dx.doi.org/10.1163/156854011x607051.
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AbstractIn the present study, a genomic DNA of MIH (GenBank: #EU869539) was cloned from the swimming crab, Portunus trituberculatus (Miers, 1876). The genome DNA, consisting of 2865 bp, is comprised of three exons interrupted by two introns. Multiple sequence alignments revealed that in the 5 upstream region of MIH, sequences with high similarity to arthropod initiator, TATA box, CREB (cyclic AMP response element binding) protein were the common structure. The signal peptide in the genomic DNA was encoded by exon1 and exon2, which was interrupted by 242 bp-intron (intron1), located between gln12 and arg13. The mature peptide was encoded by exon2 and exon3, which was interrupted by 313 bp-intron (intron2), at the position between 2nd and 3rd nucleotides of the codon encoding arg41. Pot-MIH was expressed only in the eyestalk ganglia, ovaries, testes, posterior spermatic duct, bristle in ejaculatory duct, cranial ganglia, and thoracic ganglia, as determined in various tissues by semi-quantitative RT-PCR. A cDNA encoding the mature peptide was used to express recombinant MIH (rMIH) using the Escherichia coli (Migula, 1895) expression system. Two constructs were designed to yield either a mature MIH fusion protein with and without histidine (His) tag at the carboxyl terminus. The rMIH protein was detected by SDS-PAGE and Western blot analysis, indicating that the antibody prepared by two rMIH proteins has high specificity.
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Dong, Xiaolong, Guosheng Qu, Carol Lyn Piazza, and Marlene Belfort. "Group II intron as cold sensor for self-preservation and bacterial conjugation." Nucleic Acids Research 48, no. 11 (May 7, 2020): 6198–209. http://dx.doi.org/10.1093/nar/gkaa313.
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Abstract Group II introns are self-splicing ribozymes and mobile genetic elements. Splicing is required for both expression of the interrupted host gene and intron retromobility. For the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intron's host relaxase protein. Relaxase, in turn, initiates horizontal transfer of the conjugative pRS01 plasmid and stimulates retrotransposition of the intron. Little is known about how splicing of bacterial group II introns is influenced by environmental conditions. Here, we show that low temperatures can inhibit Ll.LtrB intron splicing. Whereas autocatalysis is abolished in the cold, splicing is partially restored by the intron-encoded protein (IEP). Structure profiling reveals cold-induced disruptions of key tertiary interactions, suggesting that a kinetic trap prevents the intron RNA from assuming its native state. Interestingly, while reduced levels of transcription and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread by conjugal transfer. Taken together, this study demonstrates not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress adaptation, but also maintenance of horizontal plasmid and intron transfer under cold-shock.
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Vepritskiy, Alexey A., Inna A. Vitol, and Sandra A. Nierzwicki-Bauer. "Novel Group I Intron in the tRNALeu(UAA) Gene of a γ-Proteobacterium Isolated from a Deep Subsurface Environment." Journal of Bacteriology 184, no. 5 (March 1, 2002): 1481–87. http://dx.doi.org/10.1128/jb.184.5.1481-1487.2002.
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ABSTRACT A group I intron has been found to interrupt the anticodon loop of the tRNALeu(UAA) gene in a bacterium belonging to the γ-subdivision of Proteobacteria and isolated from a deep subsurface environment. The subsurface isolate SMCC D0715 was identified as belonging to the genus Pseudomonas. The group I intron from this isolate is the first to be reported for γ-proteobacteria, and the first instance of a tRNALeu(UAA) group I intron to be found in a group of bacteria other than cyanobacteria. The 231-nucleotide (nt) intron's sequence has group I conserved elements and folds into a bona fide group I secondary structure with canonical base-paired segments P1 to P9 and a paired region, P10. The D0715 intron possesses the 11-nt motif CCUACG … UAUGG in its P8 region, a feature not common in bacterial introns. To date, phylogenetic analysis has shown that bacterial introns form two distinct families, and their complex distribution suggests that both lateral transfer and common ancestry have taken part in the evolutionary history of these elements.
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Grivell, L. A. "Intron Mobility: Invasive introns." Current Biology 4, no. 2 (February 1994): 161–64. http://dx.doi.org/10.1016/s0960-9822(94)00039-4.
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Zumkeller, Simon, Philipp Gerke, and Volker Knoop. "A functional twintron, ‘zombie’ twintrons and a hypermobile group II intron invading itself in plant mitochondria." Nucleic Acids Research 48, no. 5 (January 9, 2020): 2661–75. http://dx.doi.org/10.1093/nar/gkz1194.
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Abstract The occurrence of group II introns in plant mitochondrial genomes is strikingly different between the six major land plant clades, contrasting their highly conserved counterparts in chloroplast DNA. Their present distribution likely reflects numerous ancient intron gains and losses during early plant evolution before the emergence of seed plants. As a novelty for plant organelles, we here report on five cases of twintrons, introns-within-introns, in the mitogenomes of lycophytes and hornworts. An internal group II intron interrupts an intron-borne maturase of an atp9 intron in Lycopodiaceae, whose splicing precedes splicing of the external intron. An invasive, hypermobile group II intron in cox1, has conquered nine further locations including a previously overlooked sdh3 intron and, most surprisingly, also itself. In those cases, splicing of the external introns does not depend on splicing of the internal introns. Similar cases are identified in the mtDNAs of hornworts. Although disrupting a group I intron-encoded protein in one case, we could not detect splicing of the internal group II intron in this ‘mixed’ group I/II twintron. We suggest the name ‘zombie’ twintrons (half-dead, half-alive) for such cases where splicing of external introns does not depend any more on prior splicing of fossilized internal introns.
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Parsch, John. "Selective Constraints on Intron Evolution in Drosophila." Genetics 165, no. 4 (December 1, 2003): 1843–51. http://dx.doi.org/10.1093/genetics/165.4.1843.
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AbstractIntron sizes show an asymmetrical distribution in a number of organisms, with a large number of “short” introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (<10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.
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Fekete, Erzsébet, Fruzsina Pénzes, Norbert Ág, Claudio Scazzocchio, Michel Flipphi, and Levente Karaffa. "Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species." Journal of Fungi 7, no. 9 (August 29, 2021): 710. http://dx.doi.org/10.3390/jof7090710.
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Spliceosomal introns are pervasive in eukaryotes. Intron gains and losses have occurred throughout evolution, but the origin of new introns is unclear. Stwintrons are complex intervening sequences where one of the sequence elements (5′-donor, lariat branch point element or 3′-acceptor) necessary for excision of a U2 intron (external intron) is itself interrupted by a second (internal) U2 intron. In Hypoxylaceae, a family of endophytic fungi, we uncovered scores of donor-disrupted stwintrons with striking sequence similarity among themselves and also with canonical introns. Intron–exon structure comparisons suggest that these stwintrons have proliferated within diverging taxa but also give rise to proliferating canonical introns in some genomes. The proliferated (stw)introns have integrated seamlessly at novel gene positions. The recently proliferated (stw)introns appear to originate from a conserved ancestral stwintron characterised by terminal inverted repeats (45–55 nucleotides), a highly symmetrical structure that may allow the formation of a double-stranded intron RNA molecule. No short tandem duplications flank the putatively inserted intervening sequences, which excludes a DNA transposition-based mechanism of proliferation. It is tempting to suggest that this highly symmetrical structure may have a role in intron proliferation by (an)other mechanism(s).
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Long, Manyuan, and Michael Deutsch. "Intron—exon structures of eukaryotic model organisms." Nucleic Acids Research 27, no. 15 (August 1, 1999): 3219–28. http://dx.doi.org/10.1093/nar/27.15.3219.
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Abstract To investigate the distribution of intron—exon structures of eukaryotic genes, we have constructed a general exon database comprising all available introncontaining genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila . We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable introns that do not contain correct splice sites, the final database contained 17 102 introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 introns per kb protein coding region. The exon distribution peaks around 30–40 residues and most introns are 40–125 nt long. The variable intron—exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total intron length per gene. For example, invertebrate introns are smaller than those of human genes, while yeast introns are shorter than invertebrate introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer introns, possibly resulting from a minimum intron size requirement for intron splicing.
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McCullough, A. J., and S. M. Berget. "G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection." Molecular and Cellular Biology 17, no. 8 (August 1997): 4562–71. http://dx.doi.org/10.1128/mcb.17.8.4562.
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Splicing of small introns in lower eucaryotes can be distinguished from vertebrate splicing by the inability of such introns to be expanded and by the inability of splice site mutations to cause exon skipping-properties suggesting that the intron rather than the exon is the unit of recognition. Vertebrates do contain small introns. To see if they possess properties similar to small introns in lower eucaryotes, we studied the small second intron from the human alpha-globin gene. Mutation of the 5' splice site of this intron resulted in in vivo intron inclusion, not exon skipping, suggesting the presence of intron bridging interactions. The intron had an unusual base composition reflective of a sequence bias present in a collection of small human introns in which multiple G triplets stud the interior of the introns. Each G triplet represented a minimal sequence element additively contributing to maximal splicing efficiency and spliceosome assembly. More importantly, G triplets proximal to a duplicated splice site caused preferential utilization of the 5' splice site upstream of the triplets or the 3' splice site downstream of the triplets; i.e., sequences containing G triplets were preferentially used as introns when a choice was possible. Thus, G triplets internal to a small intron have the ability to affect splice site decisions at both ends of the intron. Each G triplet additively contributed to splice site selectivity. We suggest that G triplets are a common component of human 5' splice sites and aid in the definition of exon-intron borders as well as overall splicing efficiency. In addition, our data suggest that such intronic elements may be characteristic of small introns and represent an intronic equivalent to the exon enhancers that facilitate recognition of both ends of an exon during exon definition.
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Mukhopadhyay, Jigeesha, and Georg Hausner. "Organellar Introns in Fungi, Algae, and Plants." Cells 10, no. 8 (August 6, 2021): 2001. http://dx.doi.org/10.3390/cells10082001.
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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.
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Rudi, Knut, and Kjetill S. Jakobsen. "Complex Evolutionary Patterns of tRNAUAALeu Group I Introns in Cyanobacterial Radiation." Journal of Bacteriology 181, no. 11 (June 1, 1999): 3445–51. http://dx.doi.org/10.1128/jb.181.11.3445-3451.1999.
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ABSTRACT Based on the findings that plastids and cyanobacteria have similar group I introns inserted into tRNAUAA Leu genes, these introns have been suggested to be immobile and of ancient origin. In contrast, recent evidence suggests lateral transfer of cyanobacterial group I introns located in tRNAUAA Leu genes. In light of these new findings, we have readdressed the evolution and lateral transfer of tRNAUAA Leu group I introns in cyanobacteral radiation. We determined the presence of introns in 38 different strains, representing the major cyanobacterial lineages, and characterized the introns in 22 of the strains. Notably, two of these strains have two tRNAUAA Leu genes, with each of these genes interrupted by introns, while three of the strains have both interrupted and uninterrupted genes. Two evolutionary distinct clusters of tRNA genes, with the genes interrupted by introns belonging to two distinct intron clusters, were identified. We also compared 16S rDNA and intron evolution for both closely and distantly related strains. The distribution of the introns in the clustered groups, as defined from 16S rDNA analysis, indicates relatively recent gain and/or loss of the introns in some of these lineages. The comparative analysis also suggests differences in the phylogenetic trees for 16S rDNA and the tRNAUAA Leu group I introns. Taken together, our results show that the evolution of the intron is considerably more complex than previous studies found to be the case. We discuss, based on our results, evolutionary models involving lateral intron transfer and models involving differential loss of the intron.
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Parenteau, Julie, Mathieu Durand, Steeve Véronneau, Andrée-Anne Lacombe, Geneviève Morin, Valérie Guérin, Bojana Cecez, et al. "Deletion of Many Yeast Introns Reveals a Minority of Genes that Require Splicing for Function." Molecular Biology of the Cell 19, no. 5 (May 2008): 1932–41. http://dx.doi.org/10.1091/mbc.e07-12-1254.
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Splicing regulates gene expression and contributes to proteomic diversity in higher eukaryotes. However, in yeast only 283 of the 6000 genes contain introns and their impact on cell function is not clear. To assess the contribution of introns to cell function, we initiated large-scale intron deletions in yeast with the ultimate goal of creating an intron-free model eukaryote. We show that about one-third of yeast introns are not essential for growth. Only three intron deletions caused severe growth defects, but normal growth was restored in all cases by expressing the intronless mRNA from a heterologous promoter. Twenty percent of the intron deletions caused minor phenotypes under different growth conditions. Strikingly, the combined deletion of all introns from the 15 cytoskeleton-related genes did not affect growth or strain fitness. Together, our results show that although the presence of introns may optimize gene expression and provide benefit under stress, a majority of introns could be removed with minor consequences on growth under laboratory conditions, supporting the view that many introns could be phased out of Saccharomyces cerevisiae without blocking cell growth.
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Nguyen, Sy Dinh, and Hunseung Kang. "Comprehensive analysis of chloroplast intron-containing genes and conserved splice sites in dicot and monocot plants." Science and Technology Development Journal - Natural Sciences 1, T1 (March 31, 2017): 60–68. http://dx.doi.org/10.32508/stdjns.v1it1.435.
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Despite the increasing knowledge on the importance of the intron splicing of chloroplast genes during plant growth and stress responses, identification of intron-containing chloroplast genes and determination of splice sites in chloroplast introns are still lacking. Here, we carried out a comprehensive analysis of the chloroplast genome sequences in important plants and crops, including four dicots (Arabidopsis thaliana, Coffea arabica, Nicotiana tabacum, and Panax schinseng) and four monocots (Musa acuminata, Oryza sativa, Triticum aestivum, and Zea mays). The results showed that both dicot and monocot chloroplast genomes harbor 6 intron-containing tRNAs (trnA, trnG, trnI, trnK, trnL, and trnV) and 10-12 intron-containing mRNAs (atpF, rpl2, rpl16, rps16, ndhA, ndhB, petB, petD, rpoC1, rps12, ycf3, and clpP). Notably, rpoC1 and clpP lacked introns in monocot plants, except M. acuminata. Analysis of the nucleotide sequences of chloroplast introns revealed that the 5’-splice sites, 3’-splice sites, and branch-point sites of the chloroplast introns were highly conserved among dicots and monocots. Notably, the 5’-splice sites and 3’-splice sites of the chloroplast introns were similar to those of the nuclear U12 introns, whereas the branch-point sites of the chloroplast introns were homologous to those of the nuclear U2 introns. Taken together, these results indicated that the chloroplast genomes contained strictly limited intron-containing genes with conserved splice sites, suggesting that splicing of chloroplast introns was important for chloroplast biogenesis and function in both dicot and monocot plants.
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Foley, Sophie, Anne Bruttin, and Harald Brüssow. "Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages." Journal of Virology 74, no. 2 (January 15, 2000): 611–18. http://dx.doi.org/10.1128/jvi.74.2.611-618.2000.
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ABSTRACT Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilusbacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillusphage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns fromLactococcus, Lactobacillus, andBacillus phages.
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Поверенная, И. В., and I. V. Poverennaya. "Intron Sliding and Length Variability of Genes Enriched of Phase 1 Long Introns." Mathematical Biology and Bioinformatics 12, no. 2 (September 19, 2017): 302–16. http://dx.doi.org/10.17537/2017.12.302.
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Due to high mutagenesis of intron sequences, intron evolution is usually considered in terms of evolution of exon-intron structures (EIS). The shifting of intron over short distances (rare evolutionary event called intron sliding) could lead to the change of intron phase, i.e. the intron position relative to the open reading frame. Here we analyze the EIS from four datasets of eukaryotic orthologues in order to find out the preferable choice of intron phase during sliding and to study the correlation between orthologous intron lengths. To identify the orthologous introns we have constructed the alignments of EIS of orthologous genes. Several sliding events with intron phase change were revealed from the analysis; however, our initial hypothesis that in the process of sliding introns prefer to change its phase to 0 more frequently, was not been confirmed. Nevertheless, it is necessary to expand the analysis on a larger dataset for making a proper conclusions. Despite high variability of intron length, some taxonomic groups share the similar length values. Moreover, some length conservation could be observed if instead of intron length L we consider a normalized length N = (L-A)/A, where A is an average length within an orthologous intron group. E.g. for ptprd genes of birds (28 species) the normalized value is in the interval (-0.15, 0.15) for 85.2 % of introns what is significantly higher than the values for random lengths set in accordance with the intron lengths distribution. That length “conservation” leads us to the question what intron length was in the ancient introns.
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Paquin, Bruno, Annette Heinfling, and David A. Shub. "Sporadic Distribution of tRNACCUArgIntrons among α-Purple Bacteria: Evidence for Horizontal Transmission and Transposition of a Group I Intron." Journal of Bacteriology 181, no. 3 (February 1, 1999): 1049–53. http://dx.doi.org/10.1128/jb.181.3.1049-1053.1999.
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ABSTRACT A group I intron interrupts the tRNACCU Arg gene of the α-purple bacterium Agrobacterium tumefaciens (B. Reinhold-Hurek and D. A. Shub, Nature [London] 357:173–176, 1992). In this study, we assess the distribution of the corresponding intron among 12 additional species of α-purple bacteria. Of 10 newly identified tRNACCU Arg genes, we found only two that contained an intron homologous to that of the AgrobacteriumtRNACCU Arg intron. This restricted and scattered distribution of the tRNACCU Arg intron among α-purple bacteria is consistent with a recent origin and horizontal transmission. Primary and secondary structural similarities between tRNAUAA Leu introns found in strains of the cyanobacterium Microcystis aeruginosa (K. Rudi and K. S. Jacobsen, FEMS Microbiol. Lett. 156:293–298, 1997) and α-purple tRNACCU Arg introns suggest that these introns share a more recent common ancestor than either does with other known cyanobacterial tRNAUAA Leu introns.
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Yan, Liuling, Mrinal Bhave, Robert Fairclough, Christine Konik, Sadequr Rahman, and Rudi Appels. "The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat." Genome 43, no. 2 (March 15, 2000): 264–72. http://dx.doi.org/10.1139/g99-117.
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Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx-TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoides (BB), by the polymerase chain reaction (PCR) approach, and from Triticum tauschii (DD), by screening a genomic DNA library. Multiple sequence alignment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extron and (or) intron structure as the previously reported waxy gene from barley. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslated leader and the entire coding region consisting of 11 exons and 10 introns. The three genes had identical lengths of exons, except exon1, and shared over 95% identity with each other within the exon regions. The majority of introns were significantly variable in length and sequence, differing mainly in length (1-57 bp) as a result of insertion and (or) deletion events. The deduced amino acid sequence from these three genes indicated that the mature WX-TMA, -TSB, and -TTD proteins contained the same number of amino acids, but differed in predicted molecular weight and isoelectric point (pI) due to amino acid substitutions (13-18). The predicted physical characteristics of the WX proteins matched the respective proteins in wheat very closely, but the match was not perfect. Furthermore the exon5 sequences of the wx-TmA, wx-TsB, and wx-TtD genes were different from a cDNA encoding a waxy gene of common wheat previously reported. The striking difference was that an insertion of 11 amino acids occurred in the cDNA sequence that could not be observed in the exons of the A, B, and D genes. It was noted, however, that the 3prime end of intron4 of these genes could account for the additional 11 amino acids. The sequence information from the available waxy genes identified the intron4-exon5-intron5 region as being diagnostic for sequence variation in waxy. The sequence variation in the waxy genes provides the basis for primer design to distinguish the respective genes in common wheat, and its progenitors, using PCR. Key words: Angiosperms, Poaceae, Triticeae, Triticum monococcum, Triticium speltoides, Triticum tauschii, granule-bound starch synthase, polymerase chain reaction (PCR), molecular evolution.
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Rudi, Knut, Tonje Fossheim, and Kjetill S. Jakobsen. "Nested Evolution of a tRNALeu(UAA) Group I Intron by both Horizontal Intron Transfer and Recombination of the Entire tRNA Locus." Journal of Bacteriology 184, no. 3 (February 1, 2002): 666–71. http://dx.doi.org/10.1128/jb.184.3.666-671.2002.
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ABSTRACT The origin and evolution of bacterial introns are still controversial issues. Here we present data on the distribution and evolution of a recently discovered divergent tRNALeu(UAA) intron. The intron shows a higher sequence affiliation with introns in tRNAIle(CAU) and tRNAArg(CCU) genes in α- and β-proteobacteria, respectively, than with other cyanobacterial tRNALeu(UAA) group I introns. The divergent tRNALeu(UAA) intron is sporadically distributed both within the Nostoc and the Microcystis radiations. The complete tRNA gene, including flanking regions and intron from Microcystis aeruginosa strain NIVA-CYA 57, was sequenced in order to elucidate the evolutionary pattern of this intron. Phylogenetic reconstruction gave statistical evidence for different phylogenies for the intron and exon sequences, supporting an evolutionary model involving horizontal intron transfer. The distribution of the tRNA gene, its flanking regions, and the introns were addressed by Southern hybridization and PCR amplification. The tRNA gene, including the flanking regions, were absent in the intronless stains but present in the intron-containing strains. This suggests that the sporadic distribution of this intron within the Microcystis genus cannot be attributed to intron mobility but rather to an instability of the entire tRNALeu(UAA) intron-containing genome region. Taken together, the complete data set for the evolution of this intron can best be explained by a model involving a nested evolution of the intron, i.e., wherein the intron has been transferred horizontally (probably through a single or a few events) to a tRNALeu(UAA) gene which is located within a unstable genome region.
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Wiebauer, K., J. J. Herrero, and W. Filipowicz. "Nuclear pre-mRNA processing in plants: distinct modes of 3'-splice-site selection in plants and animals." Molecular and Cellular Biology 8, no. 5 (May 1988): 2042–51. http://dx.doi.org/10.1128/mcb.8.5.2042-2051.1988.
Full textAbstract:
The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.
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Wiebauer, K., J. J. Herrero, and W. Filipowicz. "Nuclear pre-mRNA processing in plants: distinct modes of 3'-splice-site selection in plants and animals." Molecular and Cellular Biology 8, no. 5 (May 1988): 2042–51. http://dx.doi.org/10.1128/mcb.8.5.2042.
Full textAbstract:
The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.
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Frugoli, Julia A., Mark A. McPeek, Terry L. Thomas, and C. Robertson McClung. "Intron Loss and Gain During Evolution of the Catalase Gene Family in Angiosperms." Genetics 149, no. 1 (May 1, 1998): 355–65. http://dx.doi.org/10.1093/genetics/149.1.355.
Full textAbstract:
Abstract Angiosperms (flowering plants), including both monocots and dicots, contain small catalase gene families. In the dicot, Arabidopsis thaliana, two catalase (CAT) genes, CAT1 and CAT3, are tightly linked on chromosome 1 and a third, CAT2, which is more similar to CAT1 than to CAT3, is unlinked on chromosome 4. Comparison of positions and numbers of introns among 13 angiosperm catalase genomic sequences indicates that intron positions are conserved, and suggests that an ancestral catalase gene common to monocots and dicots contained seven introns. Arabidopsis CAT2 has seven introns; both CAT1 and CAT3 have six introns in positions conserved with CAT2, but each has lost a different intron. We suggest the following sequence of events during the evolution of the Arabidopsis catalase gene family. An initial duplication of an ancestral catalase gene gave rise to CAT3 and CAT1. CAT1 then served as the template for a second duplication, yielding CAT2. Intron losses from CAT1 and CAT3 followed these duplications. One subclade of monocot catalases has lost all but the 5′-most and 3′-most introns, which is consistent with a mechanism of intron loss by replacement of an ancestral intron-containing gene with a reverse-transcribed DNA copy of a fully spliced mRNA. Following this event of concerted intron loss, the Oryza sativa (rice, a monocot) CAT1 lineage acquired an intron in a novel position, consistent with a mechanism of intron gain at proto-splice sites.
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Nesic, D., J. Cheng, and L. E. Maquat. "Sequences within the last intron function in RNA 3'-end formation in cultured cells." Molecular and Cellular Biology 13, no. 6 (June 1993): 3359–69. http://dx.doi.org/10.1128/mcb.13.6.3359-3369.1993.
Full textAbstract:
In cultured cells, little if any mRNA accumulates from an intronless version of the human gene for triosephosphate isomerase (TPI), a gene that normally contains six introns. By deleting introns either individually or in combinations, it was demonstrated by Northern (RNA) blot hybridization that while the deletion of a greater number of introns generally results in a lower level of product mRNA, not all introns contribute equally to mRNA formation. For example, intron 1 appeared to be dispensable, at least when the remaining introns are present, but deletion of the last intron, intron 6, reduced the level of product mRNA to 51% of normal. To determine how intron 6 contributes to mRNA formation, partial deletions of intron 6 were constructed and analyzed. Deletion of the lariat and acceptor splice sites or the donor, lariat, and acceptor splice sites, each of which precluded removal of the intron 6 sequences that remained, reduced the level of product mRNA to < 1 or 27% of normal, respectively. As measured by RNase mapping and cDNA sequencing, the decrease in mRNA abundance that was attributable to the complete and partial intron 6 deletions was accompanied by an increase in the abundance of pre-mRNA that lacked a mature 3' end, i.e., that was neither cleaved nor polyadenylated. We infer from these and other data that sequences within the final intron facilitate proper 3'-end formation, possibly through an association with the components of a productive spliceosome.
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Nesic, D., J. Cheng, and L. E. Maquat. "Sequences within the last intron function in RNA 3'-end formation in cultured cells." Molecular and Cellular Biology 13, no. 6 (June 1993): 3359–69. http://dx.doi.org/10.1128/mcb.13.6.3359.
Full textAbstract:
In cultured cells, little if any mRNA accumulates from an intronless version of the human gene for triosephosphate isomerase (TPI), a gene that normally contains six introns. By deleting introns either individually or in combinations, it was demonstrated by Northern (RNA) blot hybridization that while the deletion of a greater number of introns generally results in a lower level of product mRNA, not all introns contribute equally to mRNA formation. For example, intron 1 appeared to be dispensable, at least when the remaining introns are present, but deletion of the last intron, intron 6, reduced the level of product mRNA to 51% of normal. To determine how intron 6 contributes to mRNA formation, partial deletions of intron 6 were constructed and analyzed. Deletion of the lariat and acceptor splice sites or the donor, lariat, and acceptor splice sites, each of which precluded removal of the intron 6 sequences that remained, reduced the level of product mRNA to < 1 or 27% of normal, respectively. As measured by RNase mapping and cDNA sequencing, the decrease in mRNA abundance that was attributable to the complete and partial intron 6 deletions was accompanied by an increase in the abundance of pre-mRNA that lacked a mature 3' end, i.e., that was neither cleaved nor polyadenylated. We infer from these and other data that sequences within the final intron facilitate proper 3'-end formation, possibly through an association with the components of a productive spliceosome.
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Lee, Sujin, and Scott W. Stevens. "Spliceosomal intronogenesis." Proceedings of the National Academy of Sciences 113, no. 23 (May 23, 2016): 6514–19. http://dx.doi.org/10.1073/pnas.1605113113.
Full textAbstract:
The presence of intervening sequences, termed introns, is a defining characteristic of eukaryotic nuclear genomes. Once transcribed into pre-mRNA, these introns must be removed within the spliceosome before export of the processed mRNA to the cytoplasm, where it is translated into protein. Although intron loss has been demonstrated experimentally, several mysteries remain regarding the origin and propagation of introns. Indeed, documented evidence of gain of an intron has only been suggested by phylogenetic analyses. We report the use of a strategy that detects selected intron gain and loss events. We have experimentally verified, to our knowledge, the first demonstrations of intron transposition in any organism. From our screen, we detected two separate intron gain events characterized by the perfect transposition of a reporter intron into the yeast genes RPL8B and ADH2, respectively. We show that the newly acquired introns are able to be removed from their respective pre-mRNAs by the spliceosome. Additionally, the novel allele, RPL8Bint, is functional when overexpressed within the genome in a strain lacking the Rpl8 paralogue RPL8A, demonstrating that the gene targeted for intronogenesis is functional.
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Nam, K., G. Lee, J. Trambley, S. E. Devine, and J. D. Boeke. "Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation." Molecular and Cellular Biology 17, no. 2 (February 1997): 809–18. http://dx.doi.org/10.1128/mcb.17.2.809.
Full textAbstract:
The cDNAs and genes encoding the intron lariat-debranching enzyme were isolated from the nematode Caenorhabditis elegans and the fission yeast Schizosaccharomyces pombe based on their homology with the Saccharomyces cerevisiae gene. The cDNAs were shown to be functional in an interspecific complementation experiment; they can complement an S. cerevisiae dbr1 null mutant. About 2.5% of budding yeast S. cerevisiae genes have introns, and the accumulation of excised introns in a dbr1 null mutant has little effect on cell growth. In contrast, many S. pombe genes contain introns, and often multiple introns per gene, so that S. pombe is estimated to contain approximately 40 times as many introns as S. cerevisiae. The S. pombe dbr1 gene was disrupted and shown to be nonessential. Like the S. cerevisiae mutant, the S. pombe null mutant accumulated introns to high levels, indicating that intron lariat debranching represents a rate-limiting step in intron degradation in both species. Unlike the S. cerevisiae mutant, the S. pombe dbr1::leu1+ mutant had a severe growth defect and exhibited an aberrant elongated cell shape in addition to an intron accumulation phenotype. The growth defect of the S. pombe dbr1::leu1+ strain suggests that debranching activity is critical for efficient intron RNA degradation and that blocking this pathway interferes with cell growth.
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Perlman, P., and R. Butow. "Mobile introns and intron-encoded proteins." Science 246, no. 4934 (December 1, 1989): 1106–9. http://dx.doi.org/10.1126/science.2479980.
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Ala-Kokko, L., A. P. Kvist, M. Metsäranta, K. I. Kivirikko, B. de Crombrugghe, D. J. Prockop, and E. Vuorio. "Conservation of the sizes of 53 introns and over 100 intronic sequences for the binding of common transcription factors in the human and mouse genes for type II procollagen (COL2A1)." Biochemical Journal 308, no. 3 (June 15, 1995): 923–29. http://dx.doi.org/10.1042/bj3080923.
Full textAbstract:
Over 11,000 bp of previously undefined sequences of the human COL2A1 gene were defined. The results made it possible to compare the intron structures of a highly complex gene from man and mouse. Surprisingly, the sizes of the 53 introns of the two genes were highly conserved with a mean difference of 13%. After alignment of the sequences, 69% of the intron sequences were identical. The introns contained consensus sequences for the binding of over 100 different transcription factors that were conserved in the introns of the two genes. The first intron of the gene contained 80 conserved consensus sequences and the remaining 52 introns of the gene contained 106 conserved sequences for the binding of transcription factors. The 5′-end of intron 2 in both genes had a potential for forming a stem loop in RNA transcripts.
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Landthaler, Markus, Nelson C. Lau, and David A. Shub. "Group I Intron Homing in Bacillus Phages SPO1 and SP82: a Gene Conversion Event Initiated by a Nicking Homing Endonuclease." Journal of Bacteriology 186, no. 13 (July 1, 2004): 4307–14. http://dx.doi.org/10.1128/jb.186.13.4307-4314.2004.
Full textAbstract:
ABSTRACT Many group I introns encode endonucleases that promote intron homing by initiating a double-stranded break-mediated homologous recombination event. In this work we describe intron homing in Bacillus subtilis phages SPO1 and SP82. The introns encode the DNA endonucleases I-HmuI and I-HmuII, respectively, which belong to the H-N-H endonuclease family and possess nicking activity in vitro. Coinfections of B. subtilis with intron-minus and intron-plus phages indicate that I-HmuI and I-HmuII are required for homing of the SPO1 and SP82 introns, respectively. The homing process is a gene conversion event that does not require the major B. subtilis recombination pathways, suggesting that the necessary functions are provided by phage-encoded factors. Our results provide the first examples of H-N-H endonuclease-mediated intron homing and the first demonstration of intron homing initiated by a nicking endonuclease.
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Banerjee, Shataparna, Piyush Khandelia, Geetha Melangath, Samirul Bashir, Vijaykrishna Nagampalli, and Usha Vijayraghavan. "Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly." Molecular and Cellular Biology 33, no. 16 (June 10, 2013): 3125–36. http://dx.doi.org/10.1128/mcb.00007-13.
Full textAbstract:
The multiple short introns inSchizosaccharomyces pombegenes with degeneratecissequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of theS. pombe slu7+(spslu7+) gene product, known fromSaccharomyces cerevisiaeand humanin vitroreactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3′ splice site choice during the second reaction. By using a missense mutant of this essentialS. pombefactor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3′ splice site distance, intron length, and the impact of its A/U content at the 5′ end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest inspslu7-2revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions withspprp1+, a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.
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Waldern, Justin, Nicholas J. Schiraldi, Marlene Belfort, and Olga Novikova. "Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking." Molecular Biology and Evolution 37, no. 7 (April 5, 2020): 1942–48. http://dx.doi.org/10.1093/molbev/msaa055.
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Abstract Group II (gII) introns are mobile retroelements that can spread to new DNA sites through retrotransposition, which can be influenced by a variety of host factors. To determine if these host factors bear any relationship to the genomic location of gII introns, we developed a bioinformatic pipeline wherein we focused on the genomic neighborhoods of bacterial gII introns within their native contexts and sought to determine global relationships between introns and their surrounding genes. We found that, although gII introns inhabit diverse regions, these neighborhoods are often functionally enriched for genes that could promote gII intron retention or proliferation. On one hand, we observe that gII introns are frequently found hiding in mobile elements or after transcription terminators. On the other hand, gII introns are enriched in locations in which they could hijack host functions for their movement, potentially timing expression of the intron with genes that produce favorable conditions for retrotransposition. Thus, we propose that gII intron distributions have been shaped by relationships with their surrounding genomic neighbors.
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Chen, Li-hong, Wei Yan, Ting Wang, Yu Wang, Jian Liu, and Zhuo Yu. "Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species." PLOS ONE 16, no. 3 (March 15, 2021): e0245714. http://dx.doi.org/10.1371/journal.pone.0245714.
Full textAbstract:
The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secondary structure elements designated P1-P10 helics and loops. We found a 12 nt nucleotide sequences TACCACAGGGAT at site 2 in the 3’-end of 28S rDNA, site 2 introns just insert the upstream or the downstream of the12 nt nucleotide sequences. Afters sequence analysis of all 18S and 28S rDNA introns from tested isolates, three high conserved regions around 30 nt nucleotides (conserved 1, conserved 2, conserved 3) and identical nucleotides can be found. Conserved 1, conserved 2 and conserved 3 regions have high GC content, GC percentage is almost more than 60%. From our results, it seems that the more convenient host sites, intron sequences and secondary structures, or isolates for 18S and 28S rDNA intron insertion and deletion, the more popular they are. No matter 18S rDNA introns or 18S rDNA introns among tested isolates, complementary base pairing at the splicing sites in P1-IGS-P10 tertiary helix around 5’-end introns and exons were weak.
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Stajich, Jason E., and Fred S. Dietrich. "Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformans." Eukaryotic Cell 5, no. 5 (May 2006): 789–93. http://dx.doi.org/10.1128/ec.5.5.789-793.2006.
Full textAbstract:
ABSTRACT Introns are a defining feature of eukaryotic genomes, though the mechanism of intron gain or loss is not well understood. Reverse transcription of mRNA followed by homologous recombination with the genome has been posited as a mechanism of intron loss, though little direct evidence of recent loss events has been described to support this model. We find supporting evidence for an mRNA-mediated mechanism of loss through comparative genome analyses that revealed a recent loss of 10 adjacent introns in a 22-exon gene in the human-pathogenic fungus Cryptococcus neoformans. We surveyed the gene structures of the entire genomes of Cryptococcus gattii, which diverged from the C. neoformans lineage 37 million years ago (Mya), and C. neoformans var. grubii and var. neoformans, which diverged 18 Mya. Our comparison revealed greater than 99.9% intron conservation, with evidence from 20 genes showing evidence of intron loss, but no convincing evidence of intron gain. Our findings confirm that Cryptococcus introns have been quite stable over recent evolutionary time, with occasional mRNA-mediated intron loss events.
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Kordiš, Dušan, and Janez Kokošar. "What Can Domesticated Genes Tell Us about the Intron Gain in Mammals?" International Journal of Evolutionary Biology 2012 (May 30, 2012): 1–7. http://dx.doi.org/10.1155/2012/278981.
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Domesticated genes, originating from retroelements or from DNA-transposons, constitute an ideal system for testing the hypothesis on the absence of intron gain in mammals. Since single-copy domesticated genes originated from the intronless multicopy transposable elements, the ancestral intron state for domesticated genes is zero. A phylogenomic approach has been used to analyse all domesticated genes in mammals and chordates that originated from the coding parts of transposable elements. A significant amount of intron gain was found only in domesticated genes of placental mammals, where more than 70 cases were identified. De novo gained introns show clear positional bias, since they are distributed mainly in 5′ UTR and coding regions, while 3′ UTR introns are very rare. In the coding regions of some domesticated genes up to 8 de novo gained introns have been found. Surprisingly, the majority of intron gains have occurred in the ancestor of placental mammals. Domesticated genes could constitute an excellent system on which to analyse the mechanisms of intron gain. This paper summarizes the current understanding of intron gain in mammals.
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Talerico, M., and S. M. Berget. "Intron definition in splicing of small Drosophila introns." Molecular and Cellular Biology 14, no. 5 (May 1994): 3434–45. http://dx.doi.org/10.1128/mcb.14.5.3434-3445.1994.
Full textAbstract:
Approximately half of the introns in Drosophila melanogaster are too small to function in a vertebrate and often lack the pyrimidine tract associated with vertebrate 3' splice sites. Here, we report the splicing and spliceosome assembly properties of two such introns: one with a pyrimidine-poor 3' splice site and one with a pyrimidine-rich 3' splice site. The pyrimidine-poor intron was absolutely dependent on its small size for in vivo and in vitro splicing and assembly. As such, it had properties reminiscent of those of yeast introns. The pyrimidine-rich intron had properties intermediate between those of yeasts and vertebrates. This 3' splice site directed assembly of ATP-dependent complexes when present as either an intron or exon and supported low levels of in vivo splicing of a moderate-length intron. We propose that splice sites can be recognized as pairs across either exons or introns, depending on which distance is shorter, and that a pyrimidine-rich region upstream of the 3' splice site facilitates the exon mode.
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Talerico, M., and S. M. Berget. "Intron definition in splicing of small Drosophila introns." Molecular and Cellular Biology 14, no. 5 (May 1994): 3434–45. http://dx.doi.org/10.1128/mcb.14.5.3434.
Full textAbstract:
Approximately half of the introns in Drosophila melanogaster are too small to function in a vertebrate and often lack the pyrimidine tract associated with vertebrate 3' splice sites. Here, we report the splicing and spliceosome assembly properties of two such introns: one with a pyrimidine-poor 3' splice site and one with a pyrimidine-rich 3' splice site. The pyrimidine-poor intron was absolutely dependent on its small size for in vivo and in vitro splicing and assembly. As such, it had properties reminiscent of those of yeast introns. The pyrimidine-rich intron had properties intermediate between those of yeasts and vertebrates. This 3' splice site directed assembly of ATP-dependent complexes when present as either an intron or exon and supported low levels of in vivo splicing of a moderate-length intron. We propose that splice sites can be recognized as pairs across either exons or introns, depending on which distance is shorter, and that a pyrimidine-rich region upstream of the 3' splice site facilitates the exon mode.
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Akulevičiūtė, Laura, and Rimantė Čerkauskienė. "Klinikinė frasier sindromo eiga ir atokūs rezultatai." Medicinos teorija ir praktika 21, no. 3.1 (May 18, 2015): 340–44. http://dx.doi.org/10.15591/mtp.2015.054.
Full textAbstract:
Reikšminiai žodžiai: Frasier sindromas, WT1 geno mutacija, steroidams rezistentiškas nefrozinis sindromas, gonadoblastoma. Frasier sindromas – tai retas paveldimas sindromas, kuriam būdingas steroidams atsparus nefrozinis sindromas, nefroblastoma ir gonadoblastoma, nediferencijuoti išoriniai lytiniai organai, apibūdinami kaip vyriškasis pseudohermafroditizmas arba penoskrotalinė hipospadija (XY gonadų disgenezė); gali būti tik kriptorchizmas. Sindromą lemia WT1 geno (Wilmso tumoro supresinio geno), esančio 11p13 genomo srityje, mutacijos. WT1 geno mutacijos lemia Denys-Drash arba WAGR (lytinių organų anomalijos, Wilmso auglys, aniridija, protinės raidos atsilikimas) sindromus. Frasier sindromo atveju proteinurija pasireiškia pirmaisiais gyvenimo metais, vystosi nefrozinis sindromas, progresuoja židininė segmentinė lomerulosklerozė ir inkstų nepakankamumas antrajame ar trečiajame gyvenimo dešimtmetyje. Apie 40 proc. atvejų nustatomas normalus išorinis moteriškasis fenotipas, apie 13 proc. – vyriškasis fenotipas. Aprašomas vyriškos lyties paciento klinikinis atvejis, kuris pasireiškė tipiniais Frasier sindromui būdingais simptomais – hipospadija, dešinės sėklidės hipoplazija nuo pat gimimo, steroidams atspariu nefroziniu sindromu, galutiniu inkstų funkcijos nepakankamumu, nustatytu 13 metų amžiuje. Sindromas patvirtintas nustačius heterozigotinį WT1 geno genotipą 9 introne. Šiam pacientui, nors ir buvo diagnozuotas Frasier sindromas, vyriškas pseuodohermafroditizmas nepasireiškė. Mūsų klinikinis atvejis patvirtina, kad berniukams, kuriems nuo pat gimimo nustatomos lytinių liaukų vystymosi anomalijos ir steroidams atspari židininė segmentinė glomerulosklerozė, būtina atlikti WT1 geno tyrimą, nes šiems pacientams būdinga didelė lytinių liaukų tumoro išsivystymo rizika.
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Guo, M., P. C. Lo, and S. M. Mount. "Species-specific signals for the splicing of a short Drosophila intron in vitro." Molecular and Cellular Biology 13, no. 2 (February 1993): 1104–18. http://dx.doi.org/10.1128/mcb.13.2.1104-1118.1993.
Full textAbstract:
The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.
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Guo, M., P. C. Lo, and S. M. Mount. "Species-specific signals for the splicing of a short Drosophila intron in vitro." Molecular and Cellular Biology 13, no. 2 (February 1993): 1104–18. http://dx.doi.org/10.1128/mcb.13.2.1104.
Full textAbstract:
The effects of branchpoint sequence, the pyrimidine stretch, and intron size on the splicing efficiency of the Drosophila white gene second intron were examined in nuclear extracts from Drosophila and human cells. This 74-nucleotide intron is typical of many Drosophila introns in that it lacks a significant pyrimidine stretch and is below the minimum size required for splicing in human nuclear extracts. Alteration of sequences of adjacent to the 3' splice site to create a pyrimidine stretch was necessary for splicing in human, but not Drosophila, extracts. Increasing the size of this intron with insertions between the 5' splice site and the branchpoint greatly reduced the efficiency of splicing of introns longer than 79 nucleotides in Drosophila extracts but had an opposite effect in human extracts, in which introns longer than 78 nucleotides were spliced with much greater efficiency. The white-apricot copia insertion is immediately adjacent to the branchpoint normally used in the splicing of this intron, and a copia long terminal repeat insertion prevents splicing in Drosophila, but not human, extracts. However, a consensus branchpoint does not restore the splicing of introns containing the copia long terminal repeat, and alteration of the wild-type branchpoint sequence alone does not eliminate splicing. These results demonstrate species specificity of splicing signals, particularly pyrimidine stretch and size requirements, and raise the possibility that variant mechanisms not found in mammals may operate in the splicing of small introns in Drosophila and possibly other species.
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Kennedy, C. F., and S. M. Berget. "Pyrimidine tracts between the 5' splice site and branch point facilitate splicing and recognition of a small Drosophila intron." Molecular and Cellular Biology 17, no. 5 (May 1997): 2774–80. http://dx.doi.org/10.1128/mcb.17.5.2774.
Full textAbstract:
The minimum size for splicing of a vertebrate intron is approximately 70 nucleotides. In Drosophila melanogaster, more than half of the introns are significantly below this minimum yet function well. Such short introns often lack the pyrimidine tract located between the branch point and 3' splice site common to metazoan introns. To investigate if small introns contain special sequences that facilitate their recognition, the sequences and factors required for the splicing of a 59-nucleotide intron from the D. melanogaster mle gene have been examined. This intron contains only a minimal region of interrupted pyrimidines downstream of the branch point. Instead, two longer, uninterrupted C-rich tracts are located between the 5' splice site and branch point. Both of these sequences are required for maximal in vivo and in vitro splicing. The upstream sequences are also required for maximal binding of factors to the 5' splice site, cross-linking of U2AF to precursor RNA, and assembly of the active spliceosome, suggesting that sequences upstream of the branch point influence events at both ends of the small mle intron. Thus, a very short intron lacking a classical pyrimidine tract between the branch point and 3' splice site requires accessory pyrimidine sequences in the short region between the 5' splice site and branch point.
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Kupfer, Doris M., Scott D. Drabenstot, Kent L. Buchanan, Hongshing Lai, Hua Zhu, David W. Dyer, Bruce A. Roe, and Juneann W. Murphy. "Introns and Splicing Elements of Five Diverse Fungi." Eukaryotic Cell 3, no. 5 (October 2004): 1088–100. http://dx.doi.org/10.1128/ec.3.5.1088-1100.2004.
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ABSTRACT Genomic sequences and expressed sequence tag data for a diverse group of fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, Neurospora crassa, and Cryptococcus neoformans) provided the opportunity to accurately characterize conserved intronic elements. An examination of large intron data sets revealed that fungal introns in general are short, that 98% or more of them belong to the canonical splice site (ss) class (5′GU…AG3′), and that they have polypyrimidine tracts predominantly in the region between the 5′ ss and the branch point. Information content is high in the 5′ ss, branch site, and 3′ ss regions of the introns but low in the exon regions adjacent to the introns in the fungi examined. The two yeasts have broader intron length ranges and correspondingly higher intron information content than the other fungi. Generally, as intron length increases in the fungi, so does intron information content. Homologs of U2AF spliceosomal proteins were found in all species except for S. cerevisiae, suggesting a nonconventional role for U2AF in the absence of canonical polypyrimidine tracts in the majority of introns. Our observations imply that splicing in fungi may be different from that in vertebrates and may require additional proteins that interact with polypyrimidine tracts upstream of the branch point. Theoretical protein homologs for Nam8p and TIA-1, two proteins that require U-rich regions upstream of the branch point to function, were found. There appear to be sufficient differences between S. cerevisiae and S. pombe introns and the introns of two filamentous members of the Ascomycota and one member of the Basidiomycota to warrant the development of new model organisms for studying the splicing mechanisms of fungi.
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Sandegren, Linus, and Britt-Marie Sjöberg. "Self-Splicing of the Bacteriophage T4 Group I Introns Requires Efficient Translation of the Pre-mRNA In Vivo and Correlates with the Growth State of the Infected Bacterium." Journal of Bacteriology 189, no. 3 (November 22, 2006): 980–90. http://dx.doi.org/10.1128/jb.01287-06.
Full textAbstract:
ABSTRACT Bacteriophage T4 contains three self-splicing group I introns in genes in de novo deoxyribonucleotide biosynthesis (in td, coding for thymidylate synthase and in nrdB and nrdD, coding for ribonucleotide reductase). Their presence in these genes has fueled speculations that the introns are retained within the phage genome due to a possible regulatory role in the control of de novo deoxyribonucleotide synthesis. To study whether sequences in the upstream exon interfere with proper intron folding and splicing, we inhibited translation in T4-infected bacteria as well as in bacteria containing recombinant plasmids carrying the nrdB intron. Splicing was strongly reduced for all three T4 introns after the addition of chloramphenicol during phage infection, suggesting that the need for translating ribosomes is a general trait for unperturbed splicing. The splicing of the cloned nrdB intron was markedly reduced in the presence of chloramphenicol or when translation was hindered by stop codons inserted in the upstream exon. Several exon regions capable of forming putative interactions with nrdB intron sequences were identified, and the removal or mutation of these exon regions restored splicing efficiency in the absence of translation. Interestingly, splicing of the cloned nrdB intron was also reduced as cells entered stationary phase and splicing of all three introns was reduced upon the T4 infection of stationary-phase bacteria. Our results imply that conditions likely to be frequently encountered by natural phage populations may limit the self-splicing efficiency of group I introns. This is the first time that environmental effects on bacterial growth have been linked to the regulation of splicing of phage introns.
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Wang, Guang-Dong, Yong Wang, Zhen Zeng, Jun-Ming Mao, Qin-Liu He, Qin Yao, and Ke-Ping Chen. "Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences." Evolutionary Bioinformatics 16 (January 2020): 117693432090310. http://dx.doi.org/10.1177/1176934320903108.
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Introns are well known for their high variation not only in length but also in base sequence. The evolution of intron sequences has aroused broad interest in the past decades. However, very little is known about the evolutionary pattern of introns due to the lack of efficient analytical method. In this study, we designed 2 evolutionary models, that is, mutation-and-deletion (MD) and mutation-and-insertion (MI), to simulate intron evolution using randomly generated and mutated bases by referencing to the phylogenetic tree constructed using 14 chordate introns from TF4 (transcription factor–like protein 4) gene. A comparison of attributes between model-generated sequences and chordate introns showed that the MD model with proper parameter settings could generate sequences that have attributes matchable to chordate introns, whereas the MI model with any parameter settings failed in doing so. These data suggest that the surveyed chordate introns have evolved from a long ancestral sequence through gradual reduction in length. The established methodology provides an effective measure to study the evolutionary pattern of intron sequences from organisms of various taxonomic groups. (C++ scripts of MD and MI models are available upon request.)
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Zeng, Chu, Qingsong Jiao, Ting Jia, and Xueyun Hu. "Updated Progress on Group II Intron Splicing Factors in Plant Chloroplasts." Current Issues in Molecular Biology 44, no. 9 (September 13, 2022): 4229–39. http://dx.doi.org/10.3390/cimb44090290.
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Group II introns are large catalytic RNAs (ribozymes) in the bacteria and organelle genomes of several lower eukaryotes. Many critical photosynthesis-related genes in the plant chloroplast genome also contain group II introns, and their splicing is critical for chloroplast biogenesis and photosynthesis processes. The structure of chloroplast group II introns was altered during evolution, resulting in the loss of intron self-splicing. Therefore, the assistance of protein factors was required for their splicing processes. As an increasing number of studies focus on the mechanism of chloroplast intron splicing; many new nuclear-encoded splicing factors that are involved in the chloroplast intron splicing process have been reported. This report reviewed the research progress of the updated splicing factors found to be involved in the splicing of chloroplast group II introns. We discuss the main problems that remain in this research field and suggest future research directions.
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Pidpala, O. V., and L. L. Lukash. "The analisis of human MGMT gene orthologous in protests." Faktori eksperimental'noi evolucii organizmiv 22 (September 9, 2018): 345–51. http://dx.doi.org/10.7124/feeo.v22.973.
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Aim. The intron sequences of orthologous О6-methylguanin-DNA methyltransferase (MGMT) genes in Protists on the early stages of their formation in eukaryotic organisms have been analysed. Methods. Homologous regions have been defined by the program BLASTN 2.6.1. Nucleotide sequences of the bacterial and mitochondrial group II introns have been taken from Database for Bacterial Group II Introns. Searching and identifying the MGEs have been realized by using CENSOR. Results. It has been shown that the evolution of the gene does not always coincide with the evolution of the organism. This is shown on the example of intron loss and gain in social amoebae Dictyostelium. Also it has been found the fragmentary nature of homology between various introns and exons of the orthologous genes. Conclusions. The obtained results allow offer a suggestion about the endogenous mosaic character of the evolutional formation of the gene structural units.
Keywords: О6-methylguanin-DNA methyltransferase (MGMT) gene orthologous, Protists, gene evolution, spliceosomal introns, intron loss and gain.
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Takahashi, Y., S. Urushiyama, T. Tani, and Y. Ohshima. "An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene." Molecular and Cellular Biology 13, no. 9 (September 1993): 5613–19. http://dx.doi.org/10.1128/mcb.13.9.5613-5619.1993.
Full textAbstract:
Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.
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Takahashi, Y., S. Urushiyama, T. Tani, and Y. Ohshima. "An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene." Molecular and Cellular Biology 13, no. 9 (September 1993): 5613–19. http://dx.doi.org/10.1128/mcb.13.9.5613.
Full textAbstract:
Splicing an mRNA precursor requires multiple factors involving five small nuclear RNA (snRNA) species called U1, U2, U4, U5, and U6. The presence of mRNA-type introns in the U6 snRNA genes of some yeasts led to the hypothesis that U6 snRNA may play a catalytic role in pre-mRNA splicing and that the U6 introns occurred through reverse splicing of an intron from an mRNA precursor into a catalytic site of U6 snRNA. We characterized the U2 snRNA gene of the yeast Rhodotorula hasegawae, which has four mRNA-type introns in the U6 snRNA gene, and found an mRNA-type intron of 60 bp. The intron of the U2 snRNA gene is present in the highly conserved region immediately downstream of the branch site recognition domain. Interestingly, we found that this region can form a novel base pairing with U6 snRNA. We discuss the possible implications of these findings for the mechanisms of intron acquisition and for the role of U2 snRNA in pre-mRNA splicing.