scholarly journals Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species

2021 ◽  
Vol 7 (9) ◽  
pp. 710
Author(s):  
Erzsébet Fekete ◽  
Fruzsina Pénzes ◽  
Norbert Ág ◽  
Claudio Scazzocchio ◽  
Michel Flipphi ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Inverted Repeats ◽  
Spliceosomal Introns ◽  
Symmetrical Structure ◽  
Intervening Sequences ◽  
Sequence Elements ◽  
Gains And Losses ◽  
Exon Structure ◽  
Tandem Duplications ◽  
Short Tandem

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).

scholarly journals Intron gain by tandem genomic duplication: a novel case and a modification of the traditional model

2015 ◽  
Author(s):  
Ming-Yue Ma ◽  
Deng-Ke Niu
Keyword(s):  
Sequence Similarity ◽  
Intron Gain ◽  
Spliceosomal Introns ◽  
Branch Site ◽  
Eukaryotic Gene ◽  
Exonic Splicing Enhancers ◽  
Rna Polymerase Gene ◽  
Exon Structure ◽  
Splicing Site ◽  
Genomic Duplication

Origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. Recently gained introns would be especially useful for the study of the mechanism(s) of intron gain because the evolutionary traces might have not been erased by randomly accumulated mutations. However, the mechanism(s) of intron gain remain unclear due to the presence of a few solid cases. A widely cited model of intron gain is tandem genomic duplication, in which the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. However, successful recognition and splicing of an intron require many more signals than those at the two splicing sites. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 is absent in the orthologous genes of other Solanaceae plants, and sequence similarity showed that the major part of the new intron is a direct duplication of the 3' side of the upstream intron. In addition to the new intron, a downstream exonic segment of 168bp has also been duplicated. Most of the splicing signals were inherited from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3' splicing site, two putative exonic splicing enhancers and the GC contents differentiated between the intron and exon. We propose a modified version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure.

scholarly journals SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
Luciano Carlos da Maia ◽  
Dario Abel Palmieri ◽  
Velci Queiroz de Souza ◽  
Mauricio Marini Kopp ◽  
Fernando Irajá Félix de Carvalho ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Primer Design ◽  
Cdna Sequences ◽  
Additional Information ◽  
Ssr Loci ◽  
Eukaryotic Organisms ◽  
Simple Sequence ◽  
Rice Cdna ◽  
Tandem Duplications ◽  
Short Tandem

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.

scholarly journals Intron gain by tandem genomic duplication: a novel case and a new version of the model

2016 ◽  
Author(s):  
Ming-Yue Ma ◽  
Xin-Ran Lan ◽  
Deng-Ke Niu
Keyword(s):  
Intron Gain ◽  
Spliceosomal Introns ◽  
Branch Site ◽  
Eukaryotic Gene ◽  
Exonic Splicing Enhancers ◽  
Exonic Sequence ◽  
Exon Structure ◽  
Splicing Site ◽  
Genomic Duplication ◽  
Gc Contents

Origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. Recently gained introns would be especially useful for the study of the mechanisms of intron gain because randomly accumulated mutations might erase the evolutionary traces. The mechanisms of intron gain remain unclear due to the presence of very few solid cases. A widely cited model of intron gain is tandem genomic duplication, in which the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. We found that the second intron of the potato RNA-dependent RNA polymerase gene PGSC0003DMG402000361 originated mainly from a direct duplication of the 3′ side of the upstream intron. The 5' splicing site of this new intron was recruited from the upstream exonic sequence. In addition to the new intron, a downstream exonic segment of 178 bp also arose from duplication. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers and the GC contents differentiated between the intron and exon. We propose a new version of the tandem genomic duplication model, termed as the partial duplication of the preexisting intron/exon structure. This new version and the widely cited version are not mutually exclusive.

scholarly journals Circular RNA biogenesis can proceed through an exon-containing lariat precursor

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Steven P Barrett ◽  
Peter L Wang ◽  
Julia Salzman
Keyword(s):  
Gene Expression ◽  
Mammalian Cell Culture ◽  
Circular Rna ◽  
Inverted Repeats ◽  
Systematic Effect ◽  
Eukaryotic Gene Expression ◽  
Sequence Elements ◽  
Eukaryotic Gene ◽  
Rna Biogenesis ◽  
Site Mutagenesis

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical ‘backsplicing’ event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure.

scholarly journals Complex intron generation in the yeast genus Lipomyces

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Norbert Ág ◽  
Napsugár Kavalecz ◽  
Fruzsina Pénzes ◽  
Levente Karaffa ◽  
Claudio Scazzocchio ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Intron Position ◽  
Yeast Genus ◽  
Spliceosomal Introns ◽  
Intervening Sequences ◽  
Consecutive Reactions ◽  
Donor Element ◽  
Ascomycete Yeast ◽  
Vexing Problem ◽  
Problem Sequence

AbstractIn primary transcripts of eukaryotic nuclear genes, coding sequences are often interrupted by U2-type introns. Such intervening sequences can constitute complex introns excised by consecutive splicing reactions. The origin of spliceosomal introns is a vexing problem. Sequence variation existent across fungal taxa provides means to study their structure and evolution. In one class of complex introns called [D] stwintrons, an (internal) U2 intron is nested within the 5'-donor element of another (external) U2 intron. In the gene for a reticulon-like protein in species of the ascomycete yeast genus Lipomyces, the most 5' terminal intron position is occupied by one of three complex intervening sequences consistent of differently nested U2 intron units, as demonstrated in L. lipofer, L. suomiensis, and L. starkeyi. In L. starkeyi, the donor elements of the constituent introns are abutting and the complex intervening sequence can be excised alternatively either with one standard splicing reaction or, as a [D] stwintron, by two consecutive reactions. Our work suggests how [D] stwintrons could emerge by the appearance of new functional splice sites within an extant intron. The stepwise stwintronisation mechanism may involve duplication of the functional intron donor element of the ancestor intron.

scholarly journals Downstream Sequences Influence the Choice between a Naturally Occurring Noncanonical and Closely Positioned Upstream Canonical Heptameric Fusion Motif during Bovine Coronavirus Subgenomic mRNA Synthesis

2001 ◽  
Vol 75 (16) ◽  
pp. 7362-7374 ◽  
Author(s):  
Aykut Ozdarendeli ◽  
Seulah Ku ◽  
Sylvie Rochat ◽  
Gwyn D. Williams ◽  
Savithra D. Senanayake ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Virus Genome ◽  
Intergenic Sequence ◽  
Computer Prediction ◽  
Bovine Coronavirus ◽  
Stem Loop ◽  
Upstream Site ◽  
Sequence Elements ◽  
Fusion Site

ABSTRACT Mechanisms leading to subgenomic mRNA (sgmRNA) synthesis in coronaviruses are poorly understood but are known to involve a heptameric signaling motif, originally called the intergenic sequence. The intergenic sequence is the presumed crossover region (fusion site) for RNA-dependent RNA polymerase (RdRp) during discontinuous transcription, a process leading to sgmRNAs that are both 5′ and 3′ coterminal. In the bovine coronavirus, the major fusion site for synthesis of mRNA 5 (GGUAGAC) does not conform to the canonical motif (UC[U,C]AAAC) at three positions (underlined), yet it lies just 14 nucleotides downstream from such a sequence (UCCAAAC). The infrequently used canonical sequence, by computer prediction, is buried within the stem of a stable hairpin (−17.2 kcal/mol). Here we document the existence of this stem by enzyme probing and examine its influence and that of neighboring sequences on the unusual choice of fusion sites by analyzing transcripts made in vivo from mutated defective interfering RNA constructs. We learned that (i) mutations that were predicted to unfold the stem-loop in various ways did not switch RdRp crossover to the upstream canonical site, (ii) a totally nonconforming downstream motif resulted in no measurable transcription from either site, (iii) the canonical upstream site does not function ectopically to lend competence to the downstream noncanonical site, and (iv) altering flanking sequences downstream of the downstream noncanonical motif in ways that diminish sequence similarity with the virus genome 5′ end caused a dramatic switch to the upstream canonical site. These results show that sequence elements downstream of the noncanonical site can dramatically influence the choice of fusion sites for synthesis of mRNA 5 and are interpreted as being most consistent with a mechanism of similarity-assisted RdRp strand switching during minus-strand synthesis.

scholarly journals Ks1, an epithelial cell-specific gene, responds to early signals of head formation in Hydra

Development ◽  
1994 ◽  
Vol 120 (9) ◽  
pp. 2511-2517 ◽  
Author(s):  
R. Weinziger ◽  
L.M. Salgado ◽  
C.N. David ◽  
T.C. Bosch
Keyword(s):  
Epithelial Cell ◽  
Epithelial Cells ◽  
Signal Sequence ◽  
Sequence Similarity ◽  
Specific Gene ◽  
Acid Protein ◽  
Head Formation ◽  
Sequence Elements ◽  
Messenger System ◽  
Amino Acid Protein

As a molecular marker for head specification in Hydra, we have cloned an epithelial cell-specific gene which responds to early signals of head formation. The gene, designated ks1, encodes a 217-amino acid protein lacking significant sequence similarity to any known protein. KS1 contains a N-terminal signal sequence and is rich in charged residues which are clustered in several domains. ks1 is expressed in tentacle-specific epithelial cells (battery cells) as well as in a small fraction of ectodermal epithelial cells in the gastric region subjacent to the tentacles. Treatment with the protein kinase C activator 12-O-tetradecanoylphorbol-13-acetate (TPA) causes a rapid increase in the level of ks1 mRNA in head-specific epithelial cells and also induces ectopic ks1 expression in cells of the gastric region. Sequence elements in the 5′-flanking region of ks1 that are related to TPA-responsive elements may mediate the TPA inducibility of ks1 expression. The pattern of expression of ks1 suggests that a ligand-activated diacyglycerol second messenger system is involved in head-specific differentiation.

scholarly journals Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes

2020 ◽  
Vol 12 (11) ◽  
pp. 1965-1974
Author(s):  
Hanhan Xia ◽  
Wei Zhao ◽  
Yong Shi ◽  
Xiao-Ru Wang ◽  
Baosheng Wang
Keyword(s):  
Tandem Repeat ◽  
Structural Variation ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Mitochondrial Genomes ◽  
Repeat Array ◽  
Mitochondrial Genome Evolution ◽  
Tandem Duplications ◽  
Short Tandem

Abstract Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

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