Glad you are interested. I was addressing your point of 100% ability to determine the protein sequence from the codons when RNA editing shows that the RNA may not be co-linear with DNA.
In any case, some more references....if you decide this is an interesting enough topic in itself let me know and I will start a new thread..reading some of the other posts I already see it does not fit here particularly well.
J Mol Evol. 2001 Oct-Nov;53(4-5):327-32. Related Articles, Links
Comparative analysis of RNA editing sites in higher plant chloroplasts.
Tsudzuki T, Wakasugi T, Sugiura M.
Computer Center, Aichi-Gakuin University, Araike 12, Iwasaki, Nisshin 470-0795, Japan.
Transcripts of land plant chloroplast genomes undergo C-to-U RNA editing. Systematic search disclosed 31 editing sites in tobacco, 27 in maize, and 21 in rice. Based on these identified sites, potential editing sites have been predicted in the transcripts from four angiosperm chloroplast genomes which have been completely sequenced. Most RNA editing events occur in internal codons, which result in amino-acid substitutions. The initiation codon AUG was found to be created from ACG by RNA editing in the transcripts from rpl2, psbL, and ndhD genes. Comparison of editing patterns raises a possibility that many editing sites were acquired in the evolution of angiosperms.
RNA. 2000 Oct;6(10):1339-46. Related Articles, Links
Evolution of four types of RNA editing in myxomycetes.
Horton TL, Landweber LF.
Department of Molecular Biology, Princeton University, New Jersey 08544, USA.
The myxomycete Physarum polycephalum requires extensive RNA editing to create functional mitochondrial transcripts. The cytochrome c oxidase subunit 1 (col) transcript exhibits a combination of editing forms not found together in any other eukaryotic RNA: 66 insertions of ribonucleotides (59 Cs, a single U, and three mixed dinucleotides) as well as base conversion of four Cs to Us (Gott et al., J Biol Chem, 1993, 268:25483-25486). Through a phylogenetic survey of col DNA genes and RNA transcripts in representative myxomycetes, we have decoupled the four types of editing in this lineage. Some myxomycetes share insertional editing with P. polycephalum, yet lack C--> U conversion, consistent with previous reports of separation of insertional and base conversion editing in P. polycephalum extracts (Visomirski-Robic & Gott, RNA, 1995, 3:821-837). Most remarkably, we detect unique evolutionary histories of the three different types of insertional editing, though these have been indistinguishable in vitro. For example, Clastoderma debaryanum exhibits insertions of Us, but not Cs or dinucleotides.
Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):6986-93. Related Articles, Links
Evolution of RNA editing in trypanosome mitochondria.
Simpson L, Thiemann OH, Savill NJ, Alfonzo JD, Maslov DA.
Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA. Simpson@hhmi.ucla.edu
Two different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C(34) to U(34) modification in the anticodon of the imported tRNA(Trp), thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.
There are more but most RNA editing is found in the mitochondrial genome.
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