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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.

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Positions 6 or 1′ in P and S motifs in RNA editing PPRs correlate with specific nucleotides.Depicted are individual connections of positions 6 or 1′ in those instances, where the most prominent combinatory amino acid identity correlations between positions 6 and 1′ are excluded as indicated (ex.). In these instances single amino acid positions correlate with distinct nucleotide preferences in S and P elements, respectively. For the S elements non-random distributions are found at positions 6 and 1′, for the P elements only at position 1′. The most prominent combinatory amino acid – nucleotide identity correlations which are excluded here have been identified previously (8–10).
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pone-0065343-g005: Positions 6 or 1′ in P and S motifs in RNA editing PPRs correlate with specific nucleotides.Depicted are individual connections of positions 6 or 1′ in those instances, where the most prominent combinatory amino acid identity correlations between positions 6 and 1′ are excluded as indicated (ex.). In these instances single amino acid positions correlate with distinct nucleotide preferences in S and P elements, respectively. For the S elements non-random distributions are found at positions 6 and 1′, for the P elements only at position 1′. The most prominent combinatory amino acid – nucleotide identity correlations which are excluded here have been identified previously (8–10).

Mentions: To determine whether there are additional correlations beyond these combinations, we focused the next analyses on either of these two amino acid positions individually. Accordingly we scanned nucleotide - amino acid correlations for either position with excepting the prevalent amino acid at the respective other position 6 or 1′. This approach detects amino acid - nucleotide preferences in addition to the prevalent ones (Figure 5). For example, no C and G nucleotides are found opposite amino acid N at position 1′ in S motifs. While much less prominent than the combination of amino acid identities at positions 6 and 1′, these individual positions may prefer nucleotides singly or connected with rare amino acid identities at the respective other position 6 or 1′. To identify such additional rare combinations, yet larger sample numbers are required.


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

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

Positions 6 or 1′ in P and S motifs in RNA editing PPRs correlate with specific nucleotides.Depicted are individual connections of positions 6 or 1′ in those instances, where the most prominent combinatory amino acid identity correlations between positions 6 and 1′ are excluded as indicated (ex.). In these instances single amino acid positions correlate with distinct nucleotide preferences in S and P elements, respectively. For the S elements non-random distributions are found at positions 6 and 1′, for the P elements only at position 1′. The most prominent combinatory amino acid – nucleotide identity correlations which are excluded here have been identified previously (8–10).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3675099&req=5

pone-0065343-g005: Positions 6 or 1′ in P and S motifs in RNA editing PPRs correlate with specific nucleotides.Depicted are individual connections of positions 6 or 1′ in those instances, where the most prominent combinatory amino acid identity correlations between positions 6 and 1′ are excluded as indicated (ex.). In these instances single amino acid positions correlate with distinct nucleotide preferences in S and P elements, respectively. For the S elements non-random distributions are found at positions 6 and 1′, for the P elements only at position 1′. The most prominent combinatory amino acid – nucleotide identity correlations which are excluded here have been identified previously (8–10).
Mentions: To determine whether there are additional correlations beyond these combinations, we focused the next analyses on either of these two amino acid positions individually. Accordingly we scanned nucleotide - amino acid correlations for either position with excepting the prevalent amino acid at the respective other position 6 or 1′. This approach detects amino acid - nucleotide preferences in addition to the prevalent ones (Figure 5). For example, no C and G nucleotides are found opposite amino acid N at position 1′ in S motifs. While much less prominent than the combination of amino acid identities at positions 6 and 1′, these individual positions may prefer nucleotides singly or connected with rare amino acid identities at the respective other position 6 or 1′. To identify such additional rare combinations, yet larger sample numbers are required.

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