Genome annotation in the presence of insertional RNA editing

Beargie, Christina; Liu, Tsunglin; Corriveau, Mark; Lee, Ha Youn; Gott, Jonatha M.; Bundschuh, Ralf

doi:10.1093/bioinformatics/btn487

Cited by 15 publications

(21 citation statements)

References 26 publications

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“…Dictyostelium fasciculatum does not use the UGA codon, which is rarely used by the other three dictyostelid species studied. The nad9 gene of P. polycephalum may be terminated with a UGA codon or with a UAA codon that immediately follows (Beargie et al 2008). In our study the UGA codon was never used and the UAG codon was used only once, followed closely by a UAA codon.…”

Section: Discussionmentioning

confidence: 78%

“…In the D. iridis cox2 gene, one C-to-U base change occurred along with C insertions; only C insertions occur in the cox2 gene of P. polycephalum (Gott et al 2005). The atp6 gene of P. polycephalum has a U insertion (Beargie et al 2008), but no U insertions occurred in the D. iridis atp6 gene.…”

Section: Resultsmentioning

confidence: 99%

“…This algorithm, Predictor of Insertional Editing (PIE), identified four genes in the P. polycephalum mitochondrial genome, which were undetected by typical similarity searches (Gott et al 2005). Additional bioinformatics approaches have been developed that have greatly increased the number of predicted genes in P. polycephalum (Beargie et al 2008).…”

Section: Introductionmentioning

confidence: 99%

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RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Traphagen

DiMarco²,

Silliker³

2010

RNA

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Regions of the Didymium iridis mitochondrial genome were identified with similarity to typical mitochondrial genes; however, these regions contained numerous stop codons. We used RT-PCR and DNA sequencing to determine whether, through RNA editing, these regions were transcribed into mRNAs that could encode functional proteins. Ten putative gene regions were examined: atp1, atp6, atp8, atp9, cox1, cox2, cyt b, nad4L, nad6, and nad7. The cDNA sequences of each gene could encode a functional mitochondrial protein that was highly conserved compared with homologous genes. The type of editing events and editing sequence features were very similar to those observed in the homologous genes of Physarum polycephalum, though the actual editing locations showed a variable degree of conservation. Edited sites were compared with encoded sites in D. iridis and P. polycephalum for all 10 genes. Edited sequence for a portion of the cox1 gene was available for six myxomycetes, which, when compared, showed a high degree of conservation at the protein level. Different types of editing events showed varying degrees of site conservation with C-to-U base changes being the least conserved. Several aspects of single C insertion editing events led to the preferential creation of hydrophobic amino acid codons that may help to minimize adverse effects on the resulting protein structure.

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Section: Discussionmentioning

confidence: 78%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Traphagen

DiMarco²,

Silliker³

2010

RNA

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“…The vast majority of such changes involve the specific insertion of 1-2 nucleotides (nt) (C, U, AA, UU, GC, CU, GU, or UA) at defined sites. Thus far, nearly 500 insertion sites have been identified, with another approximately 500 insertion sites predicted to occur in mitochondrial RNAs that remain to be characterized (Beargie et al 2008). Editing creates open reading frames within mRNAs and contributes to the secondary and tertiary structures of mitochondrial tRNAs and rRNAs.…”

Section: Introductionmentioning

confidence: 99%

Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria

Gott¹,

Somerlot²,

Gray³

2010

RNA

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The mitochondrial genome of Physarum polycephalum encodes five tRNAs, four of which are edited by nucleotide insertion. Two of these tRNAs, tRNA met1 and tRNA met2 , contain predicted mismatches at the beginning (proximal end) of the acceptor stem. In addition, the putative 59 end of tRNA met2 overlaps the 39 end of a small, abundant, noncoding RNA, which we term ppoRNA. These anomalies led us to hypothesize that these two Physarum mitochondrial tRNAs undergo additional editing events. Here, we show that tRNA met1 and tRNA met2 each has a nonencoded G at its 59 end. In contrast to the other nucleotides that are added to Physarum mitochondrial RNAs, these extra G residues are likely added post-transcriptionally based on (1) the absence of added G in precursor transcripts containing inserted C and AA residues, (2) the presence of potential intermediates characteristic of 59 replacement editing, and (3) preferential incorporation of GTP into tRNA molecules under conditions that do not support transcription. This is the first report of both post-transcriptional nucleotide insertions and the addition of single Gs in P. polycephalum mitochondrial transcripts. We postulate that tRNA met1 and tRNA met2 are acted upon by an activity similar to that present in the mitochondria of certain other amoebozoons and chytrid fungi, suggesting that enzymes that repair the 59 end of tRNAs may be widespread.

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“…All characterized mitochondrial mRNAs, tRNAs, and rRNAs in this acellular slime mold are subject to editing. Over 500 editing sites have been identified thus far, with another z500 sites predicted to occur in mRNAs that have yet to be characterized (Gott et al 2005;Beargie et al 2008). Most editing events involve the insertion of specific nucleotides at defined sites, leading to the creation of open reading frames in mRNAs and conserved elements within tRNAs and rRNAs.…”

Section: Introductionmentioning

confidence: 99%

Distinct roles for sequences upstream of and downstream from Physarum editing sites

Rhee

Somerlot

Parimi

et al. 2009

RNA

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RNAs in the mitochondria of Physarum polycephalum contain nonencoded nucleotides that are added during RNA synthesis. Essentially all steady-state RNAs are accurately and fully edited, yet the signals guiding these precise nucleotide insertions are presently unknown. To localize the regions of the template that are required for editing, we constructed a series of chimeric templates that substitute varying amounts of DNA either upstream of or downstream from C insertion sites. Remarkably, all sequences necessary for C addition are contained within ;9 base pairs on either side of the insertion site. In addition, our data strongly suggest that sequences within this critical region affect different steps in the editing reaction. Template alterations upstream of an editing site influence nucleotide selection and/or insertion, while downstream changes affect editing site recognition and templated extension from the added, unpaired nucleotide. The data presented here provide the first evidence that individual regions of the DNA template play discrete mechanistic roles and represent a crucial initial step toward defining the source of the editing specificity in Physarum mitochondria. In addition, these findings have mechanistic implications regarding the potential involvement of the mitochondrial RNA polymerase in the editing reaction.

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Genome annotation in the presence of insertional RNA editing

Abstract: The C source code of the programs described here are available upon request from the corresponding author.

Cited by 15 publications

References 26 publications

RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria

Distinct roles for sequences upstream of and downstream from Physarum editing sites

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