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

Traphagen, Stephen; DiMarco, Michael J.; Silliker, Margaret E.

doi:10.1261/rna.1989310

Cited by 18 publications

(10 citation statements)

References 37 publications

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“…RNA editing also occurs in the mitochondrial genome of the related plasmodial slime mold Didymium iridis (Hendrickson andSilliker 2010, Traphagen et al 2010). As expected, regions of the D. iridis mitochondrial genome that show similarity to typical mitochondrial genes (respiratory genes, ribosomal RNA genes, tRNA genes and ribosomal protein genes) contain stop codons that must be eliminated by RNA editing to make functional transcripts.…”

Section: Introductionsupporting

confidence: 58%

“…This restriction fragment also contained the 39 end of the large ribosomal subunit gene, the atp1 gene, the small ribosomal subunit gene, tRNAs met-lys-pro, and the atp9 gene (in that order) followed by the 378 bp ORF. The RNA editing sites for atp1 and atp9 genes have been reported (Traphagen et al 2010); editing sites for the small and large ribosomal subunits also have been determined (Krishnan et al 2007, Silliker unpubl data). A BLASTN query with the 378 bp ORF showed the greatest similarity to a region of the P. polycephalum genome predicted to encode the nad3 gene (3e-28, NCBI accession No.…”

Section: Resultsmentioning

confidence: 99%

“…2A) represent only a subset of the possible insertion/editing sites. The proposed C insertion sites were chosen because they aided alignment of the protein coding sequences and followed established patterns of C insertion (Gott et al 2005, Traphagen et al 2010), such as a preference for inserting in the third codon position, a preference for inserting after a purine-pyrimidine dinucleotide or after a UU dinucleotide, a preference for creating hydrophobic amino acid codons and insertion sites no closer than 9 bp apart. Once a continuous open reading frame was created through the proposed editing sites for the first 252 bp of the P. polycephalum sequence (the most conserved region of nad3 genes) the resulting protein sequence was aligned with the D. iridis ND3 protein (FIG.…”

Section: Resultsmentioning

confidence: 99%

“…Of the 16 D. iridis genes for which editing data is available only one other gene, rpS3, terminates with a TGA codon (Hendrickson and Silliker 2010). The remainder are terminated by TAA, with the exception of atp9, which is terminated by a TAG stop codon (Traphagen et al 2010). A TGA stop codon appears to terminate the nad9 gene of P. polycephalum; however the next codon, a TAA stop codon, could be the true terminator, while TGA might encode an amino acid (Beargie et al 2008).…”

Section: Resultsmentioning

confidence: 99%

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RNA editing is absent in a single mitochondrial gene ofDidymium iridis

Hendrickson¹,

Silliker

2010

Mycologia

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An open reading frame (ORF) was found in the mitochondrial genome of the Pan2-16 strain of Didymium iridis that showed high similarity to the NADH dehydrogenase subunit 3 (nad3) gene in other organisms. So far all other typical mitochondrial genes identified in this organism require RNA editing to generate ORFs capable of directing protein synthesis. The D. iridis sequence was compared to the putative nad3 gene in the related myxomycete Physarum polycephalum, which would require editing. Based on this comparison, editing sites could be predicted for the P. polycelphalum gene that would result in the synthesis of a highly conserved ND3 protein between the two organisms. To determine the editing status of the nad3 gene in other D. iridis strains, PCR was used to amplify this region from eight other independent isolates of the A1 Central American interbreeding series. In each case a 378 base pair ORF was detected by PCR amplification and sequencing. Three patterns of sequence variation were observed; however all base substitutions were in the third codon position and silent with respect to the amino acids encoded. The distribution of the sequence variants was mapped geographically. The requirement for RNA editing in all other typical mitochondrial genes of D. iridis and P. polycephalum and the presence of RNA editing in the nad3 gene of P. polycephalum suggest that the D. iridis nad3 gene might have been edited at one time. We propose that the D. iridis nad3 gene may have lost the requirement for RNA editing by reverse transcription of an edited transcript that subsequently was inserted into the genome.

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Section: Introductionsupporting

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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RNA editing is absent in a single mitochondrial gene ofDidymium iridis

Hendrickson¹,

Silliker

2010

Mycologia

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“…However, considering that Didymium mitochondrial rRNAs (16), tRNAs (2), and mRNAs Table 1. VOL. 9,2010 5S rRNA-LIKE TRANSCRIPTS IN AMOEBOZOAN MITOCHONDRIA 767 (13,15,33) are subject to editing by nucleotide insertion, any mature dniRNA likely differs from the corresponding DNA sequence.…”

Section: Downloaded Frommentioning

confidence: 99%

Abundant 5S rRNA-Like Transcripts Encoded by the Mitochondrial Genome in Amoebozoa

et al. 2010

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5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.

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Organellar RNA editing

Chateigner‐Boutin

Small

2011

WIREs RNA

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RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein diversity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles.

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

Cited by 18 publications

References 37 publications

RNA editing is absent in a single mitochondrial gene ofDidymium iridis

RNA editing is absent in a single mitochondrial gene ofDidymium iridis

Abundant 5S rRNA-Like Transcripts Encoded by the Mitochondrial Genome in Amoebozoa

Organellar RNA editing

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