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Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

van Dijk AD, Morabito G, Fiers M, van Ham RC, Angenent GC, Immink RG - PLoS Comput. Biol. (2010)

Bottom Line: Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions.We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization.The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

View Article: PubMed Central - PubMed

Affiliation: Plant Research International, Bioscience, Wageningen, The Netherlands.

ABSTRACT
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

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Interaction motifs and network evolution.The role of conservation of interaction motifs versus variation of these motifs was investigated. (A) Histogram of occurrences of interaction motifs (black) and SNPs (red) at particular positions in the protein sequences of all Arabidopsis MIKC MADS proteins. Note that there is hardly any overlap between interaction motifs and SNPs. Positions of the M, I, K and C domain are indicated. (B) Histogram of cross-species conservation of interaction motifs (black) and non-motif-sequences (red) in MIKC MADS domain protein sequences. Non-motif sequences are defined at positions in MADS protein sequences where in other MADS sequences a motif is present. (C) Four different scenarios are possible if after duplication of a MADS domain protein sequence an indel occurs in one of the two sequences: (I) indel does not overlap with a predicted interaction motif; (II) both insertion and deletion overlap with a motif; (III) only insertion or (IV) only deletion overlap with a motif. Lines indicate sequences, colored boxes indicate predicted interaction motifs, triangles indicate insertion, and arrows indicate effect of insertion/deletion on motif. As discussed in the text, if an indel overlaps a motif (scenario II-IV), in half of the cases (18% for scenario II vs 9% for each of scenario III and IV) it does not delete but only modifies the motif (illustrated by a change in color for the motif).
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pcbi-1001017-g004: Interaction motifs and network evolution.The role of conservation of interaction motifs versus variation of these motifs was investigated. (A) Histogram of occurrences of interaction motifs (black) and SNPs (red) at particular positions in the protein sequences of all Arabidopsis MIKC MADS proteins. Note that there is hardly any overlap between interaction motifs and SNPs. Positions of the M, I, K and C domain are indicated. (B) Histogram of cross-species conservation of interaction motifs (black) and non-motif-sequences (red) in MIKC MADS domain protein sequences. Non-motif sequences are defined at positions in MADS protein sequences where in other MADS sequences a motif is present. (C) Four different scenarios are possible if after duplication of a MADS domain protein sequence an indel occurs in one of the two sequences: (I) indel does not overlap with a predicted interaction motif; (II) both insertion and deletion overlap with a motif; (III) only insertion or (IV) only deletion overlap with a motif. Lines indicate sequences, colored boxes indicate predicted interaction motifs, triangles indicate insertion, and arrows indicate effect of insertion/deletion on motif. As discussed in the text, if an indel overlaps a motif (scenario II-IV), in half of the cases (18% for scenario II vs 9% for each of scenario III and IV) it does not delete but only modifies the motif (illustrated by a change in color for the motif).

Mentions: First, we compared predicted motifs with available non-synonymous single nucleotide polymorphism (SNP) data [57]. Comparison of “motif density” and “SNP density” showed that these are negatively correlated (Figure 4A). For the ∼1500 non-synonymous SNPs falling within MADS protein sequences, 170 cases were found where a SNP was located inside a motif occurrence (Table S10). Randomly generated motif occurrences with the same number of occurrences per protein as the predicted motifs were generated in 1000 trials. The average overlap of SNPs with those motif occurrences was 351+/−116, and in 965 out of 1000 random trials the overlap was larger than 170. This indicates that the experimental overlap between IMSS motifs and SNPs is significantly smaller than the randomly expected overlap (p< = 0.04; see Table S10). In addition, the cases where SNPs overlap motifs are conservative mutations (several non-conservative SNPs do affect the MADS proteins, but they fall outside the predicted interaction motifs). In fact, the largest contribution to the 170 overlaps between SNPs and motifs is formed by in total 122 SNPs found at two consecutive positions in AGL14, where an S is changed to a T and a T to an S (Ser187, Thr188). The few cases with an overlap between a potentially more important SNP and an interaction motif indicate interesting candidates for putative causes of functional differences between MADS proteins in various Arabidopsis accessions. This includes for instance a Q->E SNP in ANR1 that occurs in several ecotypes (Table S10).


Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

van Dijk AD, Morabito G, Fiers M, van Ham RC, Angenent GC, Immink RG - PLoS Comput. Biol. (2010)

Interaction motifs and network evolution.The role of conservation of interaction motifs versus variation of these motifs was investigated. (A) Histogram of occurrences of interaction motifs (black) and SNPs (red) at particular positions in the protein sequences of all Arabidopsis MIKC MADS proteins. Note that there is hardly any overlap between interaction motifs and SNPs. Positions of the M, I, K and C domain are indicated. (B) Histogram of cross-species conservation of interaction motifs (black) and non-motif-sequences (red) in MIKC MADS domain protein sequences. Non-motif sequences are defined at positions in MADS protein sequences where in other MADS sequences a motif is present. (C) Four different scenarios are possible if after duplication of a MADS domain protein sequence an indel occurs in one of the two sequences: (I) indel does not overlap with a predicted interaction motif; (II) both insertion and deletion overlap with a motif; (III) only insertion or (IV) only deletion overlap with a motif. Lines indicate sequences, colored boxes indicate predicted interaction motifs, triangles indicate insertion, and arrows indicate effect of insertion/deletion on motif. As discussed in the text, if an indel overlaps a motif (scenario II-IV), in half of the cases (18% for scenario II vs 9% for each of scenario III and IV) it does not delete but only modifies the motif (illustrated by a change in color for the motif).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2991254&req=5

pcbi-1001017-g004: Interaction motifs and network evolution.The role of conservation of interaction motifs versus variation of these motifs was investigated. (A) Histogram of occurrences of interaction motifs (black) and SNPs (red) at particular positions in the protein sequences of all Arabidopsis MIKC MADS proteins. Note that there is hardly any overlap between interaction motifs and SNPs. Positions of the M, I, K and C domain are indicated. (B) Histogram of cross-species conservation of interaction motifs (black) and non-motif-sequences (red) in MIKC MADS domain protein sequences. Non-motif sequences are defined at positions in MADS protein sequences where in other MADS sequences a motif is present. (C) Four different scenarios are possible if after duplication of a MADS domain protein sequence an indel occurs in one of the two sequences: (I) indel does not overlap with a predicted interaction motif; (II) both insertion and deletion overlap with a motif; (III) only insertion or (IV) only deletion overlap with a motif. Lines indicate sequences, colored boxes indicate predicted interaction motifs, triangles indicate insertion, and arrows indicate effect of insertion/deletion on motif. As discussed in the text, if an indel overlaps a motif (scenario II-IV), in half of the cases (18% for scenario II vs 9% for each of scenario III and IV) it does not delete but only modifies the motif (illustrated by a change in color for the motif).
Mentions: First, we compared predicted motifs with available non-synonymous single nucleotide polymorphism (SNP) data [57]. Comparison of “motif density” and “SNP density” showed that these are negatively correlated (Figure 4A). For the ∼1500 non-synonymous SNPs falling within MADS protein sequences, 170 cases were found where a SNP was located inside a motif occurrence (Table S10). Randomly generated motif occurrences with the same number of occurrences per protein as the predicted motifs were generated in 1000 trials. The average overlap of SNPs with those motif occurrences was 351+/−116, and in 965 out of 1000 random trials the overlap was larger than 170. This indicates that the experimental overlap between IMSS motifs and SNPs is significantly smaller than the randomly expected overlap (p< = 0.04; see Table S10). In addition, the cases where SNPs overlap motifs are conservative mutations (several non-conservative SNPs do affect the MADS proteins, but they fall outside the predicted interaction motifs). In fact, the largest contribution to the 170 overlaps between SNPs and motifs is formed by in total 122 SNPs found at two consecutive positions in AGL14, where an S is changed to a T and a T to an S (Ser187, Thr188). The few cases with an overlap between a potentially more important SNP and an interaction motif indicate interesting candidates for putative causes of functional differences between MADS proteins in various Arabidopsis accessions. This includes for instance a Q->E SNP in ANR1 that occurs in several ecotypes (Table S10).

Bottom Line: Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions.We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization.The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

View Article: PubMed Central - PubMed

Affiliation: Plant Research International, Bioscience, Wageningen, The Netherlands.

ABSTRACT
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.

Show MeSH