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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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Amino acids at position 6 in RNA editing PPR protein L motifs correlate with nucleotide identities.(A) Sequence logos opposite each of the four nucleotides show the amino acid identities in L domains of predicted PPR-RNA interactions at position 6. Amino acid V (valine) is prominent at all nucleotide identities and thus possibly represents non-discriminatory spacer elements. (B) Correlations between amino acid identities at position 6 are most prominent for amino acid P and to a lower extent also for L, I, T and M with nucleotide U and amino acid T (threonine) with A or G. Position 1′ shows no discernible correlation when amino acids I, L, P, T or M are present at position 6. When these amino acid identities are excluded (ex.), a weak correlation can be seen with amino acid N to nucleotide identity A or U.
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pone-0065343-g003: Amino acids at position 6 in RNA editing PPR protein L motifs correlate with nucleotide identities.(A) Sequence logos opposite each of the four nucleotides show the amino acid identities in L domains of predicted PPR-RNA interactions at position 6. Amino acid V (valine) is prominent at all nucleotide identities and thus possibly represents non-discriminatory spacer elements. (B) Correlations between amino acid identities at position 6 are most prominent for amino acid P and to a lower extent also for L, I, T and M with nucleotide U and amino acid T (threonine) with A or G. Position 1′ shows no discernible correlation when amino acids I, L, P, T or M are present at position 6. When these amino acid identities are excluded (ex.), a weak correlation can be seen with amino acid N to nucleotide identity A or U.

Mentions: Sequence logos constructed from 153 L motifs (without the L2 repeats) aligned with 258 target nucleotides show that at position 6 amino acids valine (V) and also alanine (A) are present opposite all four nucleotide identities (Figure 3A). This non-discriminating coincidence may reflect a frequent function of the L domain as spacer or placeholder that was suggested previously [9], [10].


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

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

Amino acids at position 6 in RNA editing PPR protein L motifs correlate with nucleotide identities.(A) Sequence logos opposite each of the four nucleotides show the amino acid identities in L domains of predicted PPR-RNA interactions at position 6. Amino acid V (valine) is prominent at all nucleotide identities and thus possibly represents non-discriminatory spacer elements. (B) Correlations between amino acid identities at position 6 are most prominent for amino acid P and to a lower extent also for L, I, T and M with nucleotide U and amino acid T (threonine) with A or G. Position 1′ shows no discernible correlation when amino acids I, L, P, T or M are present at position 6. When these amino acid identities are excluded (ex.), a weak correlation can be seen with amino acid N to nucleotide identity A or U.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0065343-g003: Amino acids at position 6 in RNA editing PPR protein L motifs correlate with nucleotide identities.(A) Sequence logos opposite each of the four nucleotides show the amino acid identities in L domains of predicted PPR-RNA interactions at position 6. Amino acid V (valine) is prominent at all nucleotide identities and thus possibly represents non-discriminatory spacer elements. (B) Correlations between amino acid identities at position 6 are most prominent for amino acid P and to a lower extent also for L, I, T and M with nucleotide U and amino acid T (threonine) with A or G. Position 1′ shows no discernible correlation when amino acids I, L, P, T or M are present at position 6. When these amino acid identities are excluded (ex.), a weak correlation can be seen with amino acid N to nucleotide identity A or U.
Mentions: Sequence logos constructed from 153 L motifs (without the L2 repeats) aligned with 258 target nucleotides show that at position 6 amino acids valine (V) and also alanine (A) are present opposite all four nucleotide identities (Figure 3A). This non-discriminating coincidence may reflect a frequent function of the L domain as spacer or placeholder that was suggested previously [9], [10].

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