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Scott William Roy - One of the best experts on this subject based on the ideXlab platform.
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Analysis of fungal genomes reveals commonalities of intron loss/gain and functions in intron-poor species
2020Co-Authors: Chun Shen Lim, Scott William Roy, Brooke N. Weinstein, Chris M. BrownAbstract:ABSTRACT Current evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. However, some extant eukaryotes have few Introns, raising the question as to why these few Introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species support the idea that massive intron loss has occurred in multiple clades. The intron densities estimated in the fungal ancestral states differ from zero to 8.28 Introns per one kbp of protein-coding gene. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 Introns/kbp on average, respectively), but also in diverse smuts and allies (e.g. Ustilago maydis, Meira miltonrushii and Malassezia globosa have 0.06, 0.10 and 0.20 Introns/kbp, respectively). To investigate the roles of Introns, we searched for their special characteristics using 1302 orthologous genes from eight intron-poor fungi. Notably, most of these Introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these Introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these Introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal Introns have a complex evolutionary history and underappreciated roles in gene expression.
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origin of spliceosomal Introns and alternative splicing
Cold Spring Harbor Perspectives in Biology, 2014Co-Authors: Manuel Irimia, Scott William RoyAbstract:In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal Introns. First, we briefly outline the major features of the different types of Introns, with particular emphasis on the nonspliceosomal self-splicing group II Introns, which are widely thought to be the ancestors of spliceosomal Introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal Introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.
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A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain
Molecular biology and evolution, 2007Co-Authors: Scott William Roy, David PennyAbstract:Although spliceosomal Introns are present in all characterized eukaryotes, intron numbers vary dramatically, from only a handful in the entire genomes of some species to nearly 10 Introns per gene on average in vertebrates. For all previously studied intron-rich species, significant fractions of intron positions are shared with other widely diverged eukaryotes, indicating that 1) large numbers of the Introns date to much earlier stages of eukaryotic evolution and 2) these lineages have not passed through a very intron-poor stage since early eukaryotic evolution. By the same token, among species that have lost nearly all of their ancestral Introns, no species is known to harbor large numbers of more recently gained Introns. These observations are consistent with the notion that intron-dense genomes have arisen only once over the course of eukaryotic evolution. Here, we report an exception to this pattern, in the intron-rich diatom Thalassiosira pseudonana. Only 8.1% of studied T. pseudonana intron positions are conserved with any of a variety of divergent eukaryotic species. This implies that T. pseudonana has both 1) lost nearly all of the numerous Introns present in the diatom-apicomplexan ancestor and 2) gained a large number of new Introns since that time. In addition, that so few apparently inserted T. pseudonana Introns match the positions of Introns in other species implies that insertion of multiple Introns into homologous genic sites in eukaryotic evolution is less common than previously estimated. These results suggest the possibility that intron-rich genomes may have arisen multiple times in evolution. These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich.
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Intron-rich ancestors.
Trends in genetics : TIG, 2006Co-Authors: Scott William RoyAbstract:Eukaryotic genes are interrupted by spliceosomal Introns, which are removed from gene transcripts. The number of Introns per gene varies by more than two orders of magnitude between species, implying that there has been extensive intron loss and/or gain throughout eukaryotic evolution. A recent study of intron positions in animals confirms that the ancestral bilaterian was rich in Introns, and that differences in intron number between animals largely reflect different levels of intron loss. These results refocus our attention on the evolutionary history and importance of Introns in early eukaryotic evolution.
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the evolution of spliceosomal Introns patterns puzzles and progress
Nature Reviews Genetics, 2006Co-Authors: Scott William Roy, Walter GilbertAbstract:The origins and importance of spliceosomal Introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal Introns, including the timing of intron origin and proliferation, the mechanisms by which Introns are lost and gained, and the forces that have shaped intron evolution. Recent important progress has been made in each of these areas. Patterns of intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in intron number between eukaryotic species, and studies of specific cases of intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control intron evolution.
Walter Gilbert - One of the best experts on this subject based on the ideXlab platform.
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the evolution of spliceosomal Introns patterns puzzles and progress
Nature Reviews Genetics, 2006Co-Authors: Scott William Roy, Walter GilbertAbstract:The origins and importance of spliceosomal Introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal Introns, including the timing of intron origin and proliferation, the mechanisms by which Introns are lost and gained, and the forces that have shaped intron evolution. Recent important progress has been made in each of these areas. Patterns of intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in intron number between eukaryotic species, and studies of specific cases of intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control intron evolution.
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The pattern of intron loss.
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Scott William Roy, Walter GilbertAbstract:We studied intron loss in 684 groups of orthologous genes from seven fully sequenced eukaryotic genomes. We found that Introns closer to the 3′ ends of genes are preferentially lost, as predicted if Introns are lost through gene conversion with a reverse transcriptase product of a spliced mRNA. Adjacent Introns tend to be lost in concert, as expected if such events span multiple intron positions. Directly contrary to the expectations of some, Introns that do not interrupt codons (phase zero) are more, not less, likely to be lost, an intriguing and previously unappreciated result. Adjacent Introns with matching phases are not more likely to be retained, as would be expected if they enjoyed a relative selective advantage. The findings of 3′ and phase zero intron loss biases are in direct contradiction to an extremely recent study of fungi intron evolution. All patterns are less pronounced in the lineage leading to Caenorhabditis elegans, suggesting that the process of intron loss may be qualitatively different in nematodes. Our results support a reverse transcriptase-mediated model of intron loss.
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Mystery of intron gain.
Genome research, 2003Co-Authors: Alexei Fedorov, Larisa Fedorova, Scott William Roy, Walter GilbertAbstract:For nearly 15 years, it has been widely believed that many Introns were recently acquired by the genes of multicellular organisms. However, the mechanism of acquisition has yet to be described for a single animal intron. Here, we report a large-scale computational analysis of the human, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana genomes. We divided 147,796 human intron sequences into batches of similar lengths and aligned them with each other. Different types of homologies between Introns were found, but none showed evidence of simple intron transposition. Also, 106,902 plant, 39,624 Drosophila, and 6021 C. elegans Introns were examined. No single case of homologous Introns in nonhomologous genes was detected. Thus, we found no example of transposition of Introns in the last 50 million years in humans, in 3 million years in Drosophila and C. elegans, or in 5 million years in Arabidopsis. Either new Introns do not arise via transposition of other Introns or intron transposition must have occurred so early in evolution that all traces of homology have been lost.
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The signal of ancient Introns is obscured by intron density and homolog number
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Scott William Roy, Alexei Fedorov, Walter GilbertAbstract:In ancient genes whose products have known 3-dimensional structures, an excess of phase zero Introns (those that lie between the codons) appear in the boundaries of modules, compact regions of the polypeptide chain. These excesses are highly significant and could support the hypothesis that ancient genes were assembled by exon shuffling involving compact modules. (Phase one and two Introns, and many phase zero Introns, appear to arise later.) However, as more genes, with larger numbers of homologs and intron positions, were examined, the effects became smaller, dropping from a 40% excess to an 8% excess as the number of intron positions increased from 570 to 3,328, even though the statistical significance remained strong. An interpretation of this behavior is that novel inserted positions appearing in homologs washed out the signal from a finite number of ancient positions. Here we show that this is likely to be the case. Analyses of intron positions restricted to those in genes for which relatively few intron positions from homologs are known, or to those in genes with a small number of known homologous gene structures, show a significant correlation of phase zero intron positions with the module structure, which weakens as the density of attributed intron positions or the number of homologs increases. These effects do not appear for phase one and phase two Introns. This finding matches the expectation of the mixed model of intron origin, in which a fraction of phase zero Introns are left from the assembly of the first genes, while other Introns have been added in the course of evolution.
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toward a resolution of the Introns early late debate only phase zero Introns are correlated with the structure of ancient proteins
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Sandro J De Souza, Manyuan Long, Scott William Roy, Robert J Klein, Shin Lin, Walter GilbertAbstract:We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by Introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero Introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero Introns originally present in the progenote, while almost all of the remaining intron positions correspond to Introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the Introns-early/Introns-late debate.
Manyuan Long - One of the best experts on this subject based on the ideXlab platform.
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Association of intron phases with conservation at splice site sequences and evolution of spliceosomal Introns.
Molecular biology and evolution, 1999Co-Authors: Manyuan Long, M. DeutschAbstract:How exon-intron structures of eukaryotic genes evolved under various evolutionary forces remains unknown. The phases of spliceosomal Introns (the placement of Introns with respect to reading frame) provide an opportunity to approach this question. When a large number of nuclear Introns in protein-coding genes were analyzed, it was found that most Introns were of phase 0, which keeps codons intact. We found that the phase distribution of spliceosomal Introns is strongly correlated with the sequence conservation of splice signals in exons; the relatively underrepresented phase 2 Introns are associated with the lowest conservation, the relatively overrepresented phase 0 Introns display the highest conservation, and phase 1 Introns are intermediate. Given the detrimental effect of mutations in exon sequences near splice sites as found in molecular experiments, the underrepresentation of phase 2 Introns may be the result of deleterious-mutation-driven intron loss, suggesting a possible genetic mechanism for the evolution of intron-exon structures.
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intron exon structures of eukaryotic model organisms
Nucleic Acids Research, 1999Co-Authors: Michael Deutsch, Manyuan LongAbstract:To investigate the distribution of intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available intron-containing 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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toward a resolution of the Introns early late debate only phase zero Introns are correlated with the structure of ancient proteins
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Sandro J De Souza, Manyuan Long, Scott William Roy, Robert J Klein, Shin Lin, Walter GilbertAbstract:We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by Introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero Introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero Introns originally present in the progenote, while almost all of the remaining intron positions correspond to Introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the Introns-early/Introns-late debate.
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Toward a resolution of the Introns earlyylate debate: Only phase zero Introns are correlated with the structure of ancient proteins (Introns-earlyyIntrons-lateymodules)
1998Co-Authors: Sandro J De Souza, Manyuan Long, Robert J Klein, Shin Lin, S Cott Roy, Walter GilbertAbstract:We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuff ling. These predictions are that there should be an excess of symmetric exons (and sets of exons) f lanked by Introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the bound- aries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero Introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero Introns originally present in the progenote, while almost all of the remaining intron positions correspond to Introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the Introns-earlyyIntrons-late debate. exons, or sets of exons, tend to begin and to end in the same phase, to be multiples of three bases. This argument was shown to hold at about the P 5 0.01 level (7). A second argument showed that intron positions were correlated with an aspect of the three-dimensional structure of ancient proteins, specifi- cally that intron positions were associated with compact mod- ules of diameters 21, 27, and 33 A, with P values less than 0.01 (8). Both of these regularities are predictions of any theory that holds that some or all of the Introns were used in the progenote to assemble the genes for these proteins by exon shuffling; neither of these regularities is predicted by theories which hold that the Introns were inserted into DNA by processes that are unrelated to the ultimate structure of the gene product. However, in the last year two papers have appeared that continue the argument that Introns are late. One by Cho and Doolittle (9) tries to study a possible coincidence of intron positions in gene pairs that represent duplications that oc- curred in the progenote, ancient paralogous genes to ask whether the pattern of intron positions in those genes is more suggestive of intron addition or intron loss. A second paper studying the intron distribution in a large gene family argues that the pattern observed is more one of addition or movement than loss (10). The continuing increase of DNA sequences in the public databases, increasing by a factor of two every 18 months, has led us to reinvestigate this problem using much more data. In this paper, we shall show that the statistical regularities mentioned above can now be analyzed in greater detail with much higher statistical confidence. We reaffirm the basic regularities that we saw before, but now, since there is more data, we can go further in the analysis of the correlation of Introns with three-dimensional structural elements. This fur- ther analysis shows that the strong correlation is carried by Introns that lie between codons (in phase zero), while the Introns that lie within the codons (phase one and phase two) do not show strong correlations with three-dimensional struc- ture. This analysis suggests an explicit description of intron positions in terms of both ancient Introns and later additions in a way that resolves the conflict between the two viewpoints. We conclude that about 35% of the Introns present in ancient genes are ancient, lie primarily in phase zero between codons, and are related to compact elements of protein structure, modules, ranging in diameter between 21 and 33 A. About 65% of the Introns have been added to pre-existing genes, equal fractions in each of the other phases uncorrelated to structure. This division explains why certain analyses see a large fraction of Introns as being added to previously existing genes, while the theory that the original genes were constructed through in- trons remains the simplest and strongest way of predicting the observed regularities.
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Evolution of the intron-exon structure of eukaryotic genes
Current opinion in genetics & development, 1995Co-Authors: Manyuan Long, S. J. De Souza, Walter GilbertAbstract:The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of Introns', debate the presence or absence of Introns in primordial genes. Both sides of the argument have focused on the positions of Introns with respect to protein and gene structures. A new approach has emerged in the study of the evolution of intron-exon structures: a population analysis of genes. One example is the statistical analysis of intron phases--the position of Introns within or between codons. This analysis detected a significant signal of exon shuffling in the DNA sequence database containing both ancient and modern exon sequences: intron phase correlations, that is, the association together within genes of Introns of the same phase. The results of this analysis suggest that exon shuffling played an important role in the origin of both ancient and modern genes.
Steven Zimmerly - One of the best experts on this subject based on the ideXlab platform.
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a pipeline of programs for collecting and analyzing group ii intron retroelement sequences from genbank
Mobile Dna, 2013Co-Authors: Michael Abebe, Michael A Candales, Adrian Duong, Keyar S Hood, Ryan A E Neufeld, Abat Shakenov, Runda Sun, Ashley M Jarding, Cameron Semper, Steven ZimmerlyAbstract:Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist of a ribozyme and an intron-encoded protein (IEP), are usually identified in bacterial genomes through their IEP; however, the RNA component that defines the intron boundaries is often difficult to identify because of a lack of strong sequence conservation corresponding to the RNA structure. Compounding the problem of boundary definition is the fact that a majority of group II intron copies in bacteria are truncated. Here we present a pipeline of 11 programs that collect and analyze group II intron sequences from GenBank. The pipeline begins with a BLAST search of GenBank using a set of representative group II IEPs as queries. Subsequent steps download the corresponding genomic sequences and flanks, filter out non-group II Introns, assign Introns to phylogenetic subclasses, filter out incomplete and/or non-functional Introns, and assign IEP sequences and RNA boundaries to the full-length Introns. In the final step, the redundancy in the data set is reduced by grouping Introns into sets of ≥95% identity, with one example sequence chosen to be the representative. These programs should be useful for comprehensive identification of group II Introns in sequence databases as data continue to rapidly accumulate.
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group ii Introns mobile ribozymes that invade dna
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Alan M. Lambowitz, Steven ZimmerlyAbstract:Group II Introns are mobile ribozymes that self-splice from precursor RNAs to yield excised intron lariat RNAs, which then invade new genomic DNA sites by reverse splicing. The Introns encode a reverse transcriptase that stabilizes the catalytically active RNA structure for forward and reverse splicing, and afterwards converts the integrated intron RNA back into DNA. The characteristics of group II Introns suggest that they or their close relatives were evolutionary ancestors of spliceosomal Introns, the spliceosome, and retrotransposons in eukaryotes. Further, their ribozyme-based DNA integration mechanism enabled the development of group II Introns into gene targeting vectors (“targetrons”), which have the unique feature of readily programmable DNA target specificity.
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Mobile Group II Introns
Annual Review of Genetics, 2004Co-Authors: Alan M. Lambowitz, Steven ZimmerlyAbstract:Mobile group II Introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the intron-encoded protein. After DNA insertion, the Introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II Introns. We also discuss recently discovered links between group II intron mobility and DNA replication, new insights into group II intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II Introns and both eukaryotic spliceosomal Introns and non-LTR-retrotransposons. Finally, we describe the development of mobile group II Introns into gene-targeting vectors, "targetrons," which have programmable target specificity.
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Mobile group II Introns.
Annual Review of Genetics, 2004Co-Authors: Alan M. Lambowitz, Steven ZimmerlyAbstract:▪ Abstract Mobile group II Introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the intron-encoded protein. After DNA insertion, the Introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II Introns. We also discuss recently discovered links between group II intron mobility and DNA replication, new insights into group II intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II Introns and both eukaryotic spliceosomal ...
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Identification of a family of group II Introns encoding LAGLIDADG ORFs typical of group I Introns.
RNA (New York N.Y.), 2002Co-Authors: Navtej Toor, Steven ZimmerlyAbstract:Group I and group II Introns are unrelated classes of Introns that each encode proteins that facilitate intron splicing and intron mobility. Here we describe a new subfamily of nine Introns in fungi that are group II Introns but encode LAGLIDADG ORFs typical of group I Introns. The Introns have fairly standard group IIB1 RNA structures and are inserted into three different sites in SSU and LSU rRNA genes. Therefore, Introns should not be assumed to be group I Introns based solely on the presence of a LAGLIDADG ORF.
Kehou Pan - One of the best experts on this subject based on the ideXlab platform.
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heterogeneity of intron presence absence in olifantiella sp bacillariophyta contributes to the understanding of intron loss
Journal of Phycology, 2018Co-Authors: Jichang Han, Lin Zhang, Pu Wang, Guanpin Yang, Song Wang, Kehou PanAbstract:Although hypotheses have been proposed and developed to interpret the origins and functions of Introns, substantial controversies remain about the mechanism of intron evolution. The availability of Introns in the intermediate state is quite helpful for resolving this debate. In this study, a new strain of diatom (denominated as DB21-1) was isolated and identified as Olifantiella sp., which possesses multiple types of 18S rDNAs (obtained from genomic DNA; lengths ranged from 2,056 bp to 2,988 bp). Based on alignments between 18S rDNAs and 18S rRNA (obtained from cDNA; 1,783 bp), seven intron insertion sites (IISs) located in the 18S rDNA were identified, each of which displayed the polymorphism of intron presence/absence. Specific primers around each IIS were designed to amplify the Introns and the results indicated that Introns in the same IIS varied in lengths, while terminal sequences were conserved. Our study showed that the process of intron loss happens via a series of successive steps, and each step could derive corresponding Introns under intermediate states. Moreover, these results indicate that the mechanism of genomic deletion that occurs at DNA level can also lead to exact intron loss.
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Heterogeneity of intron presence/absence in Olifantiella sp. (Bacillariophyta) contributes to the understanding of intron loss.
Journal of phycology, 2017Co-Authors: Han Jichang, Pu Wang, Guanpin Yang, Song Wang, Zhang Lin, Kehou PanAbstract:Although hypotheses have been proposed and developed to interpret the origins and functions of Introns, substantial controversies remain about the mechanism of intron evolution. The availability of Introns in the intermediate state is quite helpful for resolving this debate. In this study, a new strain of diatom (denominated as DB21-1) was isolated and identified as Olifantiella sp., which possesses multiple types of 18S rDNAs (obtained from genomic DNA; lengths ranged from 2,056 bp to 2,988 bp). Based on alignments between 18S rDNAs and 18S rRNA (obtained from cDNA; 1,783 bp), seven intron insertion sites (IISs) located in the 18S rDNA were identified, each of which displayed the polymorphism of intron presence/absence. Specific primers around each IIS were designed to amplify the Introns and the results indicated that Introns in the same IIS varied in lengths, while terminal sequences were conserved. Our study showed that the process of intron loss happens via a series of successive steps, and each step could derive corresponding Introns under intermediate states. Moreover, these results indicate that the mechanism of genomic deletion that occurs at DNA level can also lead to exact intron loss.
