Limits...
Improved computational target site prediction for pentatricopeptide repeat RNA editing factors.

Takenaka M, Zehrmann A, Brennicke A, Graichen K - PLoS ONE (2013)

Bottom Line: Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles.Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported.PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs.

View Article: PubMed Central - PubMed

Affiliation: Molekulare Botanik, Universität Ulm, Ulm, Germany. mizuki.takenaka@uni-ulm.de

ABSTRACT
Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique sequence motif 5' of their target editing sites. Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported. PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs. We now find that inclusion of these motifs improves the prediction of RNA editing target sites. Previously overlooked RNA editing target sites are suggested from the PPR motif structures of known E-class PPR proteins and are experimentally verified. RNA editing target sites are assigned for the novel PPR protein MEF32 (mitochondrial editing factor 32) and are confirmed in the cDNA.

Show MeSH
Inclusion of L, L2 and S2 repeats generally improves the prediction accuracy of RNA editing targets.Although the bona fide target sites are listed in the top ranks even without including the L, L2 and S2 repeats, their consideration mostly improves the prediction accuracy if only slightly. This suggests that these repeats also connect to target RNA sequences. Shown here are only the data for Arabidopsis. For Physcomitrella mitochondria, prediction ranks target sites always at the top, but then there are only very few editing sites in this moss (Figure S3). (A) Prediction of the target sites for the known chloroplast editing factors finds the identified targets within the top ranks out of the 34 RNA editing sites in chloroplasts of Arabidopsis. Prediction from only the P and S repeats (□) is usually sufficient, but inclusion of the L, L2 and S2 elements (•) often improves the ranking. (B) Analogous improvements of the predictions are seen within the 430 editing sites considered for mitochondrial PPR proteins. In a few instances the predicted PPR-RNA interaction drops in rank when the L, L2 and S2 elements are included (e.g. the targets of MEF18 and MEF19; further details are given in Figure S3). The nad6-95 target site of MEF8 (asterisk) cannot be ranked since the p-value is >1 in the FIMO program evaluation.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3675099&req=5

pone-0065343-g007: Inclusion of L, L2 and S2 repeats generally improves the prediction accuracy of RNA editing targets.Although the bona fide target sites are listed in the top ranks even without including the L, L2 and S2 repeats, their consideration mostly improves the prediction accuracy if only slightly. This suggests that these repeats also connect to target RNA sequences. Shown here are only the data for Arabidopsis. For Physcomitrella mitochondria, prediction ranks target sites always at the top, but then there are only very few editing sites in this moss (Figure S3). (A) Prediction of the target sites for the known chloroplast editing factors finds the identified targets within the top ranks out of the 34 RNA editing sites in chloroplasts of Arabidopsis. Prediction from only the P and S repeats (□) is usually sufficient, but inclusion of the L, L2 and S2 elements (•) often improves the ranking. (B) Analogous improvements of the predictions are seen within the 430 editing sites considered for mitochondrial PPR proteins. In a few instances the predicted PPR-RNA interaction drops in rank when the L, L2 and S2 elements are included (e.g. the targets of MEF18 and MEF19; further details are given in Figure S3). The nad6-95 target site of MEF8 (asterisk) cannot be ranked since the p-value is >1 in the FIMO program evaluation.

Mentions: Figure 7 shows the rankings of the predicted RNA editing target sites of the presently published RNA editing factors as listed in Figure S3. Both approaches rank the known target sites for each RNA editing factor in the upper 50% in plastids (Figure 7A) as well as in mitochondria (Figure 7B). However, the ranking of many sites improves considerably when the L, L2 and S2 motifs are included. For example, one the two experimentally identified target sites of CLB19, rpoA-200, is predicted at position three of 34 plastid editing sites when only the P and S codes are used (Figure 7A). Inclusion of the L, L2 and S2 elements increases the prediction of this site to rank two. Overall, in plastids, the predictions of nine target sites improve by inclusion of the L, L2 and S2 motifs, eleven target sites are equally well predicted without these motifs, and three predictions are better with only the P and S elements.


Improved computational target site prediction for pentatricopeptide repeat RNA editing factors.

Takenaka M, Zehrmann A, Brennicke A, Graichen K - PLoS ONE (2013)

Inclusion of L, L2 and S2 repeats generally improves the prediction accuracy of RNA editing targets.Although the bona fide target sites are listed in the top ranks even without including the L, L2 and S2 repeats, their consideration mostly improves the prediction accuracy if only slightly. This suggests that these repeats also connect to target RNA sequences. Shown here are only the data for Arabidopsis. For Physcomitrella mitochondria, prediction ranks target sites always at the top, but then there are only very few editing sites in this moss (Figure S3). (A) Prediction of the target sites for the known chloroplast editing factors finds the identified targets within the top ranks out of the 34 RNA editing sites in chloroplasts of Arabidopsis. Prediction from only the P and S repeats (□) is usually sufficient, but inclusion of the L, L2 and S2 elements (•) often improves the ranking. (B) Analogous improvements of the predictions are seen within the 430 editing sites considered for mitochondrial PPR proteins. In a few instances the predicted PPR-RNA interaction drops in rank when the L, L2 and S2 elements are included (e.g. the targets of MEF18 and MEF19; further details are given in Figure S3). The nad6-95 target site of MEF8 (asterisk) cannot be ranked since the p-value is >1 in the FIMO program evaluation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3675099&req=5

pone-0065343-g007: Inclusion of L, L2 and S2 repeats generally improves the prediction accuracy of RNA editing targets.Although the bona fide target sites are listed in the top ranks even without including the L, L2 and S2 repeats, their consideration mostly improves the prediction accuracy if only slightly. This suggests that these repeats also connect to target RNA sequences. Shown here are only the data for Arabidopsis. For Physcomitrella mitochondria, prediction ranks target sites always at the top, but then there are only very few editing sites in this moss (Figure S3). (A) Prediction of the target sites for the known chloroplast editing factors finds the identified targets within the top ranks out of the 34 RNA editing sites in chloroplasts of Arabidopsis. Prediction from only the P and S repeats (□) is usually sufficient, but inclusion of the L, L2 and S2 elements (•) often improves the ranking. (B) Analogous improvements of the predictions are seen within the 430 editing sites considered for mitochondrial PPR proteins. In a few instances the predicted PPR-RNA interaction drops in rank when the L, L2 and S2 elements are included (e.g. the targets of MEF18 and MEF19; further details are given in Figure S3). The nad6-95 target site of MEF8 (asterisk) cannot be ranked since the p-value is >1 in the FIMO program evaluation.
Mentions: Figure 7 shows the rankings of the predicted RNA editing target sites of the presently published RNA editing factors as listed in Figure S3. Both approaches rank the known target sites for each RNA editing factor in the upper 50% in plastids (Figure 7A) as well as in mitochondria (Figure 7B). However, the ranking of many sites improves considerably when the L, L2 and S2 motifs are included. For example, one the two experimentally identified target sites of CLB19, rpoA-200, is predicted at position three of 34 plastid editing sites when only the P and S codes are used (Figure 7A). Inclusion of the L, L2 and S2 elements increases the prediction of this site to rank two. Overall, in plastids, the predictions of nine target sites improve by inclusion of the L, L2 and S2 motifs, eleven target sites are equally well predicted without these motifs, and three predictions are better with only the P and S elements.

Bottom Line: Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles.Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported.PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs.

View Article: PubMed Central - PubMed

Affiliation: Molekulare Botanik, Universität Ulm, Ulm, Germany. mizuki.takenaka@uni-ulm.de

ABSTRACT
Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique sequence motif 5' of their target editing sites. Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported. PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs. We now find that inclusion of these motifs improves the prediction of RNA editing target sites. Previously overlooked RNA editing target sites are suggested from the PPR motif structures of known E-class PPR proteins and are experimentally verified. RNA editing target sites are assigned for the novel PPR protein MEF32 (mitochondrial editing factor 32) and are confirmed in the cDNA.

Show MeSH