The<i>in vivo</i>use of alternate 3′-splice sites in group I introns

Sellem, Carole H.; Belcour, Léon

doi:10.1093/nar/22.7.1135

Cited by 14 publications

(6 citation statements)

References 23 publications

(20 reference statements)

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“…Splicing of the upstream intron component could generate a transcript whereby the downstream located ORF is fused in frame with the upstream exon, optimizing the expression of the downstream intron-encoded LAGLIDADG protein, a scenario we refer to as splicing-mediated core creep ( Guha et al, 2018 ) where transcripts are generated that fuse the downstream located ORF sequence with the upstream exon. Similar splicing patterns demonstrating the “plasticity” of intron RNA folds have been previously observed ( Sellem and Belcour, 1994 ; Turk et al, 2013 ). Tandem type complex introns, such as O. ips cox3 i2, have been observed and described in the literature ( Deng et al, 2016 ; Zubaer et al, 2018 ).…”

Section: Discussionsupporting

confidence: 85%

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

et al. 2021

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Fungi assigned to the Ophiostomatales are of economic concern as many are blue-stain fungi and some are plant pathogens. The mitogenomes of two blue-stain fungi, Ophiostoma minus and Ophiostoma piliferum, were sequenced and compared with currently available mitogenomes for other members of the Ophiostomatales. Species representing various genera within the Ophiostomatales have been examined for gene content, gene order, phylogenetic relationships, and the distribution of mobile elements. Gene synteny is conserved among the Ophiostomatales but some members were missing the atp9 gene. A genome wide intron landscape has been prepared to demonstrate the distribution of the mobile genetic elements (group I and II introns and homing endonucleases) and to provide insight into the evolutionary dynamics of introns among members of this group of fungi. Examples of complex introns or nested introns composed of two or three intron modules have been observed in some species. The size variation among the mitogenomes (from 23.7 kb to about 150 kb) is mostly due to the presence and absence of introns. Members of the genus Sporothrix sensu stricto appear to have the smallest mitogenomes due to loss of introns. The taxonomy of the Ophiostomatales has recently undergone considerable revisions; however, some lineages remain unresolved. The data showed that genera such as Raffaelea appear to be polyphyletic and the separation of Sporothrix sensu stricto from Ophiostoma is justified.

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Section: Discussionsupporting

confidence: 85%

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

et al. 2021

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“…Sci. USA 96 (1999) group I introns, whereby fungal mitochondrial introns bring their upstream exons into phase with their internal ORFs by occasional use of an alternative 3Ј splice site located between the ORF and the conserved intron core (11,(32)(33)(34).…”

Section: Discussionmentioning

confidence: 99%

Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes

Landthaler

Shub

1999

Proc. Natl. Acad. Sci. U.S.A.

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Analysis of RNA that can be labeled with GTP indicates the existence of group I introns in genes of at least three transcriptional classes in the genome of Staphylococcus aureus bacteriophage Twort. A single ORF of 142 amino acids (Orf142) is interrupted by three self-splicing group I introns, providing the first example of a phage gene with multiple intron insertions. Twort Orf142 is encoded in a message that is abundant 15-20 min after infection and is highly similar to a late gene product (Orf8) of the morphologically related Listeria phage A511. The introns in orf142 are spliced in vivo and contain all the conserved features of primary sequence and secondary structure of group I introns in subgroup IA2, which includes the introns in Escherichia coli phage T4 and the Bacillus phages ␤22 and SPO1. Introns I2 and I3 in orf142 are highly similar, and their intron insertion sites are closely spaced. The presence of transcripts with a skipped exon between these introns indicates that they may fold into a single active ribozyme resulting in alternative splicing. Alternatively, the cleaved 5 exon preceding I2 may undergo trans splicing to the 3 exon that follows I3. Regardless of the detailed mechanism, these results demonstrate a new means whereby a single gene can give rise to multiple messenger RNAs.Group I introns interrupt tRNA, rRNA, and protein-coding genes. Most group I introns have been found in mitochondrial DNA, but they are also present in chloroplasts and eukaryotic viruses, in nuclear rRNA genes of various protists and other lower eukaryotes, and in eubacteria and their phages (1, 2). Most of the previously described group I introns in bacteriophages are inserted in genes coding for proteins involved in DNA synthesis. Introns in E. coli phage T4 are present in nrdB (3, 4) and nrdD͞sunY (5), which code for ribonucleotide reductases and td, encoding thymidylate synthase (6). In the Bacillus phage ␤22, the thymidylate synthase (thy) gene is also interrupted by a group I intron that is highly similar to the T4 td intron (7), whereas the introns of the closely related Bacillus phages SPO1, SP82, and are inserted in the coding regions of the DNA polymerase gene (8). Recently group I introns were also found in genes that are expressed late during infection, the terminase (terL) gene of Lactobacillus phage LL-H (9) and orf40 of Lactococcus phage r1t (10).Group I introns share a common secondary structure and conserved sequence elements that form the catalytic core (11). The splicing pathway involves two consecutive transesterifications. The first reaction is initiated by a nucleophilic attack by the 3Ј OH of exogenous guanosine at the 5Ј splice site, resulting in a covalent linkage of the noncoded guanosine to the 5Ј end of the intron (12). The reaction pathway can be used to detect self-splicing group I introns by incubating deproteinized RNA with radio-labeled GTP in vitro (13). GTP labeling led to the discovery of a number of group I introns in phages (3,14) and in the tRNA genes of various eubacter...

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“…For a number of Euglena introns and twintrons, including those in rpl16, rpoC1, ycf8, and roaA genes, a small proportion of splicing occurs at alternative 5Ј or 3Ј junctions, usually producing a truncated protein due to introduced frame shifts (Copertino et al 1992;Hong and Hallick 1994;Jenkins et al 1995). Alternative splicing has also been reported for some group I introns (Wallweber et al 1997;Landthaler and Shub 1999;Vader et al 2002), and in one case, alternative splicing may be responsible for translation of the maturase ORF encoded within the group I intron (Sellem and Belcour 1994).…”

Section: Discussionmentioning

confidence: 80%

Principles of 3′ splice site selection and alternative splicing for an unusual group II intron from Bacillus anthracis

Robart

Montgomery²,

Smith³

et al. 2004

RNA

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We investigated the self-splicing properties of two introns from the bacterium Bacillus anthracis. One intron (B.a.I1) splices poorly in vitro despite having typical structural motifs, while the second (B.a.I2) splices well while having apparently degenerated features. The spliced exons of B.a.I2 were sequenced, and splicing was found to occur at a 3 site shifted one nucleotide from the expected position, thus restoring missing ␥-␥ and IBS3-EBS3 pairings, but leaving the two conserved exonic ORFs out of frame. Because of the unexpected splice site, the principles for 3 intron definition were examined, which showed that the 3 splice site is flexible but contingent on ␥-␥ and IBS3-EBS3 pairings, and can be as far away as four nucleotides from the wild-type site. Surprisingly, alternative splicing occurs at position +4 for wild-type B.a.I2 intron, both in vitro and in vivo, and the alternative event fuses the two conserved exon ORFs, presumably leading to translation of the downstream ORF. The finding suggests that the structural irregularities of B.a.I2 may be an adaptation to facilitate gene expression in vivo.

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Thein vivouse of alternate 3′-splice sites in group I introns

Cited by 14 publications

References 23 publications

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes

Principles of 3′ splice site selection and alternative splicing for an unusual group II intron from Bacillus anthracis

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