NORMAL GENOMIC

• Hausner G, Monteiro-Vitorello CB, Searles DB, Maland M, Fulbright DW, Bertrand H
• A long open reading frame in the mitochondrial LSU rRNA group-I intron ofCryphonectria parasitica encodes a putative S5 ribosomal protein fused toa maturase.
• Curr Genet. 1999; 35: 109-17
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• A 4238-bp intervening sequence within the highly conserved U11 region ofthe mitochondrial large subunit ribosomal RNA gene of the fungusCryphonectria parasitica Ep155 has been sequenced and identified to be agroup-I intron. This is the largest group-I intron reported to-date forfungal mitochondrial genomes. The intron contains an 851-codon openreading frame encoding a putative, but complete, small-subunit ribosomalprotein of 510 amino acids which is fused at its carboxyl terminus to a311 amino-acid polypeptide representing a typical maturase-like protein. Ashort open reading frame of 83 amino acids with some similarity tomaturases, but lacking a translation-initiation codon, was also noted atthe 3' end of the intron. The unusual size of the intron and thearrangement of the open and truncated reading frames suggest that thissegment of the mtDNA of C. parasitica has arisen by a fusion of componentsfrom two or more different introns, possibly involving the re-location ofintronic genes.

• Sainsard-Chanet A, Begel O, Belcour L
• DNA double-strand break in vivo at the 3' extremity of exons locatedupstream of group II introns. Senescence and circular DNA introns inPodospora mitochondria.
• J Mol Biol. 1994; 242: 630-43
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• In the filamentous fungus Podospora anserina, the unavoidable phenomenonof senescence is associated with the amplification of the first intron ofthe mitochondrial cox1 that accumulates as circular DNA moleculesconsisting of tandem repeats. This group II intron (cox1-i1 or alpha) isable to transpose and contains an open reading frame with significantamino acid similarity with reverse transcriptases. The generation of theseintronic circular DNA molecules, their amplification and their involvementin the senescence process are unresolved questions. We demonstrate herethat: (1) another group II intron, the fourth intron of gene cox1,cox1-i4, is also able to give precise DNA end to end junctions; (2) thisintronic sequence can be found amplified during senescence, although to alesser extent than cox1-i1; (3) the amplification of the DNA multimericcox1-i1 molecules likely does not proceed by autonomous replication; (4)the generation of the DNA intronic circles does not require efficientintron splicing; (5) a DNA double-strand break occurs in vivo at the 3'extremity of the cox1-e1 and cox1-e4 exons preceding the group II intronsthat form circular DNAs. On the whole, these results show that the abilityto form DNA circular molecules is a property of some group II introns andthey demonstrate the occurrence of a specific DNA cleavage at or near theintegration site of these group II introns. The results strongly suggestthat this cleavage is involved in the formation of the group II intronicDNA circles and could also be involved in the phenomenon of group IIintron homing.

• Sainsard-Chanet A, Begel O, Belcour L
• DNA deletion of mitochondrial introns is correlated with the process ofsenescence in Podospora anserina.
• J Mol Biol. 1993; 234: 1-7
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• In the filamentous fungus Podospora anserina, the unavoidable phenomenonof senescence is associated with specific mitochondrial rearrangements andparticularly with the amplification of some regions of the mitochondrialchromosome. Mechanisms responsible for these rearrangements are stillunknown. The implication in this phenomenon, of the first intron of themitochondrial gene cox1 (intron alpha), a class II intron that presentssignificant amino acid similarity with retroviral reverse transcriptases,was postulated several years ago. We demonstrate here by polymerase chainreaction experiments: (1) that senescent and young cultures contain DNAmolecules precisely deleted for intronic sequences; (2) that thesedeletions are found to a much greater extent in senescent than in youngcultures; (3) that DNA intron deletion likely results from a reversetranscriptase-mediated mechanism as indicated by the detection of copiesof the gene 1 cox1 completely devoid of its 15 introns; (4) that theintron alpha-encoded protein could intervene in this process. On thewhole, these results strongly suggest that in Podospora, an increase in amitochondrial reverse transcriptase activity probably mediated by theintron alpha-encoded protein is involved in the process of senescence.

• Knoop V, Brennicke A
• A mitochondrial intron sequence in the 5'-flanking region of a plantnuclear lectin gene.
• Curr Genet. 1991; 20: 423-5
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• A sequence fragment from the cis-splicing intron between exons a and b ofthe NADH-dehydrogenase subunit 5 gene (nad5) in plant mitochondria is alsopresent in one of two closely related nuclear-encoded lectin genes ofDolichos biflorus. This sequence of 116 nucleotides is the majordifference in the 5'-flanking region of two recently described lectingenes (Harada et al. 1990). The stem and leaf lectin DB58 does not containthe insert, while the otherwise more than 90% identical 5'-flanking regionof the seed lectin is interrupted by this mitochondrial intron sequence.

• Wahleithner JA, MacFarlane JL, Wolstenholme DR
• A sequence encoding a maturase-related protein in a group II intron of aplant mitochondrial nad1 gene.
• Proc Natl Acad Sci U S A. 1990; 87: 548-52
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• We have determined from nucleotide sequence analysis that the subterminaland terminal exons of a respiratory chain NADH dehydrogenase subunit Igene in broad bean mitochondrial DNA (mtDNA) are separated by a group IIintron. Within this intron is a 687-codon open reading frame that, fromconsiderations of similarity between amino acid sequences predicted fromthis open reading frame and maturase-coding sequences in group II intronsof certain fungal mitochondrial genes, appears to encode amaturase-related protein. Transcripts complementary to this broad beansequence (designated a mat-r gene) were detected among RNAs isolated frombroad bean mitochondria. Data obtained from DNA-DNA hybridizationsindicated that soybean and corn mtDNAs also contain a mat-r gene andsuggested that only one copy of this gene occurs in each plant mtDNA. Theputative protein specified by the broad bean mat-r gene contains aminoacid sequences characteristic of reverse transcriptases. Because of this,consideration is given to the possibility that the maturase-relatedprotein may be functional in the mechanisms by which plant mtDNA sequencesare rearranged and foreign sequences are incorporated into plant mtDNAs.

• Lamb MR et al.
• Functional domains in introns. RNA processing intermediates in cis- andtrans-acting mutants in the penultimate intron of the mitochondrial genefor cytochrome b.
• J Biol Chem. 1983; 258: 1991-9
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• The penultimate intron of the split mitochondrial gene (cob) forapocytochrome b of Saccharomyces cerevisiae is of particular interest; itcontains a long unassigned reading frame, is present in both long form(six exons) and short form (three exons) of the gene, and a productexpressed from it is required for the removal of its transcript and thatof an intron in the transcript of the oxi3 gene. Complementation analysisshows mutants in this intron to be either cis-dominant or transrecessive.Cis-dominant mutants are located in the first third (approximately 350base pairs) of the open and near the 3'-end of the closed reading frame,while trans-recessive mutants are scattered throughout the remainingtwo-thirds (approximately 750 base pairs) of the open frame. Mutants inboth classes exhibit the same pattern of splicing defects in theirtranscripts, but for different reasons. Those in the trans-recessive classlack a functional maturase (probably a protein of Mr = 27,000) encodedwholly within the 3'-terminal segment of the intron, and for this reasonalso fail to express oxi3. In contrast, cis-dominant mutants are incapableof providing the splicing complex with a substrate of appropriate 2degrees structure. They also accumulate a novel transcript, 1900nucleotides long, which contains the intron fused to the downstream (3')exons. This may reflect an inability of the splicing complex to completethe normal sequence of cleavage of the intron at its downstream junctionand the ligation of the two exonic moieties.