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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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Structure model of RNA editing PPR proteins and their alignment to the RNA editing target sequence.The RNA editing PPR proteins are extended at their C-termini by E and often also by DYW domains. Different from P-type PPR proteins, the RNA editing PPR proteins contain alternating P-L-S type elements. The positions of the amino acid identities at positions 6 and 1′ are not given in the structurally correct position. These two amino acid positions have here been correlated to nucleotide identities (Figure S1). Dashed lines indicate their presumed connection to target nucleotide identities. Position 1′ is the first amino acid of the respective C-terminally adjacent repeat. For element S2 this position corresponds to amino acid 33 of this repeat while the E domain begins by convention only after amino acid 36. To illustrate this unclear assignment we placed position 1′ for the S2 element between the S2 and E domains. Question marks indicate the connections to the L, S2 and L2 domains investigated here for correlations with the opposite nucleotides. The nucleotide sequence is arbitrary and is spelled out solely to indicate the specific order of nucleotides here.
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pone-0065343-g001: Structure model of RNA editing PPR proteins and their alignment to the RNA editing target sequence.The RNA editing PPR proteins are extended at their C-termini by E and often also by DYW domains. Different from P-type PPR proteins, the RNA editing PPR proteins contain alternating P-L-S type elements. The positions of the amino acid identities at positions 6 and 1′ are not given in the structurally correct position. These two amino acid positions have here been correlated to nucleotide identities (Figure S1). Dashed lines indicate their presumed connection to target nucleotide identities. Position 1′ is the first amino acid of the respective C-terminally adjacent repeat. For element S2 this position corresponds to amino acid 33 of this repeat while the E domain begins by convention only after amino acid 36. To illustrate this unclear assignment we placed position 1′ for the S2 element between the S2 and E domains. Question marks indicate the connections to the L, S2 and L2 domains investigated here for correlations with the opposite nucleotides. The nucleotide sequence is arbitrary and is spelled out solely to indicate the specific order of nucleotides here.

Mentions: The L, L2 and S2 type motifs characteristic for RNA editing PPR proteins were not included in previous analyses. To investigate their potential contact with selected nucleotide identities, we analysed amino acid positions 6 and 1′ in all classes of repeat units in 41 PPR RNA editing factors and aligned them with the respective nucleotides in the upstream sequences of their target RNA editing sites (Figure 1 and Figure S1). Amino acids 6 and 1′ correspond to the sixth amino acid of the considered PPR motif and the first amino acid of the next C-terminal PPR motif which is accordingly termed 1′ (or 33), respectively (Figure 1 and Figure S1). To position the RNA, the fourth nucleotide upstream of each editing site (nucleotide –4) was aligned to the S2 motif. The S2 element is located directly N-terminal of the E motif. The PPR elements N-terminally following the S2 motif were aligned consecutively with the subsequent upstream (5′) nucleotides. In three separate considerations, amino acids at either position 6 or 1′ or the combination of amino acids at both positions were recorded with respect to the corresponding nucleotides.


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

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

Structure model of RNA editing PPR proteins and their alignment to the RNA editing target sequence.The RNA editing PPR proteins are extended at their C-termini by E and often also by DYW domains. Different from P-type PPR proteins, the RNA editing PPR proteins contain alternating P-L-S type elements. The positions of the amino acid identities at positions 6 and 1′ are not given in the structurally correct position. These two amino acid positions have here been correlated to nucleotide identities (Figure S1). Dashed lines indicate their presumed connection to target nucleotide identities. Position 1′ is the first amino acid of the respective C-terminally adjacent repeat. For element S2 this position corresponds to amino acid 33 of this repeat while the E domain begins by convention only after amino acid 36. To illustrate this unclear assignment we placed position 1′ for the S2 element between the S2 and E domains. Question marks indicate the connections to the L, S2 and L2 domains investigated here for correlations with the opposite nucleotides. The nucleotide sequence is arbitrary and is spelled out solely to indicate the specific order of nucleotides here.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3675099&req=5

pone-0065343-g001: Structure model of RNA editing PPR proteins and their alignment to the RNA editing target sequence.The RNA editing PPR proteins are extended at their C-termini by E and often also by DYW domains. Different from P-type PPR proteins, the RNA editing PPR proteins contain alternating P-L-S type elements. The positions of the amino acid identities at positions 6 and 1′ are not given in the structurally correct position. These two amino acid positions have here been correlated to nucleotide identities (Figure S1). Dashed lines indicate their presumed connection to target nucleotide identities. Position 1′ is the first amino acid of the respective C-terminally adjacent repeat. For element S2 this position corresponds to amino acid 33 of this repeat while the E domain begins by convention only after amino acid 36. To illustrate this unclear assignment we placed position 1′ for the S2 element between the S2 and E domains. Question marks indicate the connections to the L, S2 and L2 domains investigated here for correlations with the opposite nucleotides. The nucleotide sequence is arbitrary and is spelled out solely to indicate the specific order of nucleotides here.
Mentions: The L, L2 and S2 type motifs characteristic for RNA editing PPR proteins were not included in previous analyses. To investigate their potential contact with selected nucleotide identities, we analysed amino acid positions 6 and 1′ in all classes of repeat units in 41 PPR RNA editing factors and aligned them with the respective nucleotides in the upstream sequences of their target RNA editing sites (Figure 1 and Figure S1). Amino acids 6 and 1′ correspond to the sixth amino acid of the considered PPR motif and the first amino acid of the next C-terminal PPR motif which is accordingly termed 1′ (or 33), respectively (Figure 1 and Figure S1). To position the RNA, the fourth nucleotide upstream of each editing site (nucleotide –4) was aligned to the S2 motif. The S2 element is located directly N-terminal of the E motif. The PPR elements N-terminally following the S2 motif were aligned consecutively with the subsequent upstream (5′) nucleotides. In three separate considerations, amino acids at either position 6 or 1′ or the combination of amino acids at both positions were recorded with respect to the corresponding nucleotides.

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