A model for RNA editing in kinetoplastid mitochondria: RNA molecules transcribed from maxicircle DNA provide the edited information

RNA editing in wheat mitochondria proceeds by a deamination mechanism

“…These results argue against the involvement of nucleic acids in plant mitochondrial RNA editing. It has been reported that inhibition of enzyme activities by micrococcal nuclease can be explained by a substrate masking effect [17]. A similar result has been observed in the apolipoprotein B editing system [18].…”

“…The involvement of RNA guides in the RNA editing process in trypanosomes [17] has prompted the search of such cofactors in the case of the other editing processes. Our previous preliminary results showed that treatment of the wheat mitochondrial lysate with micrococcal nuclease partially reduced the editing activity [13] suggesting the presence of a nucleic acid factor involved in plant mitochondrial editing.…”

The evolution of cellular computing: nature’s solution to a computational problem

“…The genetic information for editing is stored in the form of 'guide' RNA molecules (gRNAs), very small (50-70 nt) transcripts that mediate editing by base-pairing with specific regions of the edited transcript, exploiting G:U base-pairs in RNA (Blum et al, 1990). Each gRNA contains the sequence information to edit approximately 30 nt of edited RNA and pairs more efficiently with the final product than with the pre-edited substrate.…”

“…Editing by each guide RNA creates an anchor sequence for binding the next guide RNA (Fig. 10, Blum et al, 1990;Maslov and Simpson, 1992) leading to an ordered cascade of insertion and deletion editing events. RNA editing is thus a cellular process which uses RNA sequences as guides to convert seemingly disordered RNA sequences into a final messenger RNA molecule: a truly RNA-based computer.…”

Sequence bias in edited kinetoplastid RNAs

“…The single-celled flagellated organisms in the order Kinetoplastidae posttranscriptionally remodel the sequences of many of their mitochondrially encoded transcripts by the precise insertion and deletion of uridylates (Us)+ These sequence changes are directed by small trans-acting guide RNAs (gRNAs) that are complementary (by both Watson-Crick and G:U base pairing) to edited sequences (Blum et al+, 1990; for recent reviews, see Alfonzo et al+, 1997;Kable et al+, 1997;Sloof & Benne, 1997)+ The insertion and deletion of Us in kinetoplastid RNAs (kRNAs) creates the functional open reading frames as is evident from the homology of the proteins predicted from translation of edited mRNAs to proteins encoded in the mitochondria of numerous other organisms+ In the kinetoplastid parasite, Trypanosoma brucei, 12 of the 18 mitochondrially encoded pre-mRNAs are edited to varying degrees, many extensively, resulting in a total of 1,362 editing sites (Arts & Benne, 1996, and references therein)+ This quantity of editing is predicted to require hundreds of gRNAs, each specifying the editing of 4 to 10 sites and resulting in complementarity to an ;45-nt stretch of edited RNA+ Although only a small fraction of gRNAs have been sequenced, renaturation kinetic analyses of the coding capacity of the minicircle component of mitochondrial DNA of T. brucei predicts more than enough capacity for the number of different gRNAs required to specify all the observed editing (Stuart, 1993)+ The mechanism by which gRNAs direct the insertion and deletion of Us follows a cleavage/U addition or removal/ligation pathway initially proposed by Blum et al+ (1990)+ gRNAs appear to select the site to be processed by forming a short duplex adjacent to the editing site+ Editing is initiated by endonucleolytic cleavage of the pre-mRNA 39 (with respect to gRNA) to the terminus of this duplex, generating upstream and downstream pre-mRNA cleavage fragments+ For clarity, the positions that are 59 and 39, with respect to pre-mRNA, of the editing site will be referred to as upstream and downstream, respectively+ After cleavage, the 39 terminus of the upstream fragment is processed by U addition or removal during insertion and deletion editing, respectively, and then the fragments are rejoined+ Each round of editing at a site in vitro is specified by the gRNA sequence opposing it (Cruz-Reyes & SollnerWebb, 1996;Kable et al+, 1996;Seiwert et al+, 1996)+ During U deletion, the cleavage occurs downstream of the Us to be deleted (Cruz-Reyes & Sollner-Webb, 1996;Siewert et al+, 1996), and the Us are removed by a U-specific 39 exonuclease until the first non-U nucleotide is encountered (S+ Lawson, unpubl+ data)+ Thus, the site of gRNA-directed cleavage and the specificity of the exonuclease can account for the number of Us deleted+ How the gRNA directs the addition of the appropriate number of Us during insertion editing appears more complex+ Insertion sites are edited by insertion of anywhere from 1 to 13 Us (Benne, 1994)+ Accuracy in the number of Us inserted is e...…”