RNA editing is absent in a single mitochondrial gene of Didymium iridis

LITERATURE CITED

• Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. 1997. Gapped BLAST and psi-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402.
   Google Scholar
• Antes T, Costandy H, Mahendran R, Spottswood M, Miller D. 1998. Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes. Mol Cell Biol 18:7521–7527.
   Google Scholar
• Beargie C, Liu T, Corriveau M, Lee HY, Gott J, Bundschuh R. 2008. Genome annotation in the presence of insertional RNA editing. Bioinformatics 24:2571–2578.
   Google Scholar
• Benne R, Burg J, Brakenhoff J, Sloof P, van Boom J, Tromp M. 1986. Major transcript of the frameshifted coxII gene from trypanosoma mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46: 819–826.
   Google Scholar
• Bundschuh R. 2004. Computational prediction of RNA editing sites. Bioinformatics 20:3214–3220.
   Google Scholar
• ———. 2007. Computational approaches to insertional RNA editing. Methods Enzymol 424:173–195.
   Google Scholar
• Byrne EM, Gott JM. 2002. Cotranscriptional editing of Physarum mitochondrial RNA requires local features of the native template. RNA 8:1174–1185.
   Google Scholar
• ———, ———. 2004. Unexpectedly complex editing patterns at dinucleotide insertion sites in Physarum mitochondria. Mol Cell Biol 24:7821–7828.
   Google Scholar
• Cheng YW, Visomirski-Robic LM, Gott JM. 2001. Non-templated addition of nucleotides to the 3′ end of nascent RNA during RNA editing in Physarum. Embo J 20:1405–1414.
   Google Scholar
• Clark J, Collins ONR, Tang H-C. 1991. Didymium iridis mating systems: partial compatibility between mating series. Mycologia 83:210–213.
   Google Scholar
• ———, Landolt JC. 1993. Didymium iridis reproductive systems: additions and meiotic drive. Mycologia 85:764–768.
   Google Scholar
• ———, Stephenson SL. 1990. Didymium iridis reproductive systems: new additions. Mycologia 82:274–276.
   Google Scholar
• Collins ONR. 1976. Heterothallism and homothallism: a study of 27 isolates of Didymium iridis, a true slime mold. Am J Bot 63:138–143.
   Google Scholar
• Covello PS, Gray MW. 1993. On the evolution of RNA editing. Trends Genet 9:265–268.
   Google Scholar
• Gott JM. 2003. Expanding genome capacity via rna editing. CR Biol 326:901–908.
   Google Scholar
• ———, Emeson RB. 2000. Functions and mechanisms of RNA editing. Annu Rev Genet 34:499–531.
   Google Scholar
• ———, Rhee AC. 2008. Insertion/deletion editing in Physarum polycephalum. In: Goringer HU, ed., RNA editing. Nucleic Acids Mol Biol 20:85–104.
   Google Scholar
• ———, Parimi N, Bundschuh R. 2005. Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucl Acids Res 33:5063–5072.
   Google Scholar
• ———, Visomirski LM, Hunter JL. 1993. Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J Biol Chem 268:25483–25486.
   Google Scholar
• Gray M. 2003. Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55:227–233.
   Google Scholar
• ———. 2009. RNA editing in plant mitochondria: 20 years later. IUBMB Life 61:1101–1104.
   Google Scholar
• Heidel AJ, Glockner G. 2008. Mitochondrial genome evolution in the social amoebae. Mol Biol Evol 25: 1440–1450.
   Google Scholar
• Hendrickson PG, Silliker ME. 2010. RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis. CurrGene. Curr Genet 56:203–213.
   Google Scholar
• Horton TL, Landweber LF. 2000. Evolution of four types of rna editing in myxomycetes. RNA 6:1339–1346.
   Google Scholar
• Itchoda N, Nishizawa S, Nagano H, Kubo T, Mikami T. 2002. The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales. Theor Appl Genet 104:209–213.
   Google Scholar
• Krishnan U, Barsamian A, Miller DL. 2007. Evolution of RNA editing sites in the mitochondrial small subunit rRNA of the myxomycota. Methods Enzymol 424:197–220.
   Google Scholar
• Krishnasamy S, Grant RA, Makaroff CA. 1994. Subunit 6 of the Fo-ATP synthase complex from cytoplasmic male-sterile radish: RNA editing and NH2-terminal protein sequencing. Pl Mol Biol 24:129–141.
   Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and ClustalX version 2. Bioinformatics 23: 2947–2948.
   Google Scholar
• Lopez L, Picardi E, Quagliariello C. 2007. RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales. Biochimie 89:159–167.
   Google Scholar
• Lu MZ, Szmidt AE, Wang XR. 1998. RNA editing in gymnosperms and its impact on the evolution of the mitochondrial coxI gene. Plant Mol Biol 37:225–234.
   Google Scholar
• Mahendran R, Spottswood MR, Miller DL. 1991. RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature 349:434–438.
   Google Scholar
• Marchler-Bauer A, et al. 2009. Cdd: specific functional annotation with the conserved domain database. Nucl Acids Res 37:D205–210.
   Google Scholar
• Maslov DA, Avila HA, Lake JA, Simpson L. 1994. Evolution of RNA editing in kinetoplastid protozoa. Nature 368: 345–348.
   Google Scholar
• Miller D, Mahendran R, Spottswood M, Costandy H, Wang S, Ling M-l, Yang N. 1993. Insertional editing in mitochondria of Physarum. Sem Cell Biol 4:261–266.
   Google Scholar
• Miller ML, Miller DL. 2008. Non-DNA-templated addition of nucleotides to the 3′ end of RNAs by the mitochondrial RNAa polymerase of Physarum polycephalum. Mol Cell Biol 28:5795–5802.
   Google Scholar
• Nakagawa CC, Jones EP, Miller DL. 1998. Mitochondrial DNA rearrangements associated with mF plasmid integration and plasmodial longevity in Physarum polycephalum. Curr Genet 33:178–187.
   Google Scholar
• Nomura H, Moriyama Y, Kawano S. 2005. Rearrangements in the Physarum polycephalum mitochondrial genome associated with a transition from linear mF-mtDNA recombinants to circular molecules. Curr Genet 47: 100–110.
   Google Scholar
• Rhee AC, Somerlot BH, Parimi N, Gott JM. 2009. Distinct roles for sequences upstream of and downstream from Physarum editing sites. RNA 15:1753–1765.
   Google Scholar
• Scheer MA, Silliker ME. 2006. Mitochondrial inheritance patterns in Didymium iridis are not influenced by stage of mating competency. Mycologia 98:51–56.
   Google Scholar
• Silliker ME, Gong T, Collins OR. 1988. Spore-to-spore cultivation of Didymium iridis on heat-killed bacteria. Mycologia 80:151–156.
   Google Scholar
• ———, Liles JL, Monroe JA. 2002. Patterns of mitochondrial inheritance in the myxogastrid Didymium iridis. Mycologia 94:939–946.
   Google Scholar
• Speijer D. 2008. Evolution aspects of RNA editing. Nucleic Acids Mol Biol 20:199–227.
   Google Scholar
• Takano H, Abe T, Sakurai R, Moriyama Y, Miyazawa Y, Nozaki H, Kawano S, Sasaki N, Kuroiwa T. 2001. The complete DNA sequence of the mitochondrial genome of Physarum polycephalum. Mol Gen Genet 264:539–545.
   Google Scholar
• ———, Kawano S, Kuroiwa T. 1992. Constitutive homologous recombination between mitochondrial DNA and a linear mitochondrial plasmid in Physarum polycephalum. Curr Genet 22:221–227.
   Google Scholar
• Traphagen SJ, DiMarco MJ, Silliker ME. 2010. RNA editing of ten Didymium iridis mitochondrial genes and comparison to the homologous genes in Physarum polycephalum. RNA 16:828–838.
   Google Scholar
• Visomirski-Robic LM, Gott JM. 1995. Accurate and efficient insertional RNA editing in isolated Physarum mitochondria. RNA 1:681–691.
   Google Scholar
• ———, ———. 1997a. Insertional editing in isolated Physarum mitochondria is linked to RNA synthesis. RNA 3:821–837.
   Google Scholar
• ———, ———. 1997b. Insertional editing of nascent mitochondrial RNAs in Physarum. Proc Natl Acad Sci USA 94:4324–4329.
   Google Scholar