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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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Mechanism of generating protein-protein interaction diversity by shifting intron/exon borders.(A) After a duplication of a gene or in the case of alternative splicing, a shift of an intron/exon border can modify a protein interaction motif which overlaps or is close to such a border. Top panel, schematic illustration of this process. Line indicates gene sequence, grey bars indicate exons, and colored bars indicate predicted interaction motifs. Bottom panel, part of a protein sequence alignment for the Arabidopsis MADS domain protein SHORT VEGETATIVE PHASE (SVP1) and an identified alternatively spliced SVP form named SVP3. A predicted interaction motif in SVP1 which is almost completely spliced out in SVP3 is shown in red. Two grey bars indicate the two adjacent exons. (B) Predicted interaction motifs can be either close to an intron/exon border (indicated by red motif) or far away from the intron/exon border (green motif). Bars in the graph indicate average number of Arabidopsis MIKC MADS proteins in which predicted interaction motifs occur for two different motif groups: motifs that are located close to the intron/exon border (<3 amino acids distance, red) occur on average in a few proteins only, and motifs that are located far away from the border (> = 3 amino acids distance, green) occur in many proteins.
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pcbi-1001017-g005: Mechanism of generating protein-protein interaction diversity by shifting intron/exon borders.(A) After a duplication of a gene or in the case of alternative splicing, a shift of an intron/exon border can modify a protein interaction motif which overlaps or is close to such a border. Top panel, schematic illustration of this process. Line indicates gene sequence, grey bars indicate exons, and colored bars indicate predicted interaction motifs. Bottom panel, part of a protein sequence alignment for the Arabidopsis MADS domain protein SHORT VEGETATIVE PHASE (SVP1) and an identified alternatively spliced SVP form named SVP3. A predicted interaction motif in SVP1 which is almost completely spliced out in SVP3 is shown in red. Two grey bars indicate the two adjacent exons. (B) Predicted interaction motifs can be either close to an intron/exon border (indicated by red motif) or far away from the intron/exon border (green motif). Bars in the graph indicate average number of Arabidopsis MIKC MADS proteins in which predicted interaction motifs occur for two different motif groups: motifs that are located close to the intron/exon border (<3 amino acids distance, red) occur on average in a few proteins only, and motifs that are located far away from the border (> = 3 amino acids distance, green) occur in many proteins.

Mentions: Interestingly, the interaction motifs in the ‘hotspot region’ at the junction between MADS and I domain overlap an intron/exon boundary. This provides a plausible evolutionary mechanism to generate protein interaction diversity by shifting these intron/exon boundaries after duplications or via alternative splicing (Figure 5). Indeed the above mentioned cases where indels modify interaction motifs in duplicated proteins occur often in the MADS domain protein ‘hotspot region’, in which interaction motifs overlap an intron/exon boundary. An example of a change in interaction pattern via ‘splicing out’ of a predicted interaction motif is observed in a recently identified SVP splicing variant (named SVP3; Accession: EU078686; Figure 5). SVP3 lost the interaction motif found in the hotspot region of the fully spliced SVP protein (SVP1) leading to a large loss of protein interaction partners (Figure 5; Table 1; Figure S2). Additional discussion is provided in the Supplementary information (Text S1, Figure S1), where we also provide an analysis of the distance of predicted interaction motifs from intron/exon boundaries. Based on these findings we hypothesize that shifting intron/exon borders plays a role in neo-functionalization of plant MADS domain transcription factors by direct changing of dimerization capacity (Figure 5). Note that, at least in the above-mentioned SVP case, this mechanism seems to allow the duplicate to optimize in one specific interaction and avoid conflict with the original copy, by deleting other common interactions.


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)

Mechanism of generating protein-protein interaction diversity by shifting intron/exon borders.(A) After a duplication of a gene or in the case of alternative splicing, a shift of an intron/exon border can modify a protein interaction motif which overlaps or is close to such a border. Top panel, schematic illustration of this process. Line indicates gene sequence, grey bars indicate exons, and colored bars indicate predicted interaction motifs. Bottom panel, part of a protein sequence alignment for the Arabidopsis MADS domain protein SHORT VEGETATIVE PHASE (SVP1) and an identified alternatively spliced SVP form named SVP3. A predicted interaction motif in SVP1 which is almost completely spliced out in SVP3 is shown in red. Two grey bars indicate the two adjacent exons. (B) Predicted interaction motifs can be either close to an intron/exon border (indicated by red motif) or far away from the intron/exon border (green motif). Bars in the graph indicate average number of Arabidopsis MIKC MADS proteins in which predicted interaction motifs occur for two different motif groups: motifs that are located close to the intron/exon border (<3 amino acids distance, red) occur on average in a few proteins only, and motifs that are located far away from the border (> = 3 amino acids distance, green) occur in many proteins.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2991254&req=5

pcbi-1001017-g005: Mechanism of generating protein-protein interaction diversity by shifting intron/exon borders.(A) After a duplication of a gene or in the case of alternative splicing, a shift of an intron/exon border can modify a protein interaction motif which overlaps or is close to such a border. Top panel, schematic illustration of this process. Line indicates gene sequence, grey bars indicate exons, and colored bars indicate predicted interaction motifs. Bottom panel, part of a protein sequence alignment for the Arabidopsis MADS domain protein SHORT VEGETATIVE PHASE (SVP1) and an identified alternatively spliced SVP form named SVP3. A predicted interaction motif in SVP1 which is almost completely spliced out in SVP3 is shown in red. Two grey bars indicate the two adjacent exons. (B) Predicted interaction motifs can be either close to an intron/exon border (indicated by red motif) or far away from the intron/exon border (green motif). Bars in the graph indicate average number of Arabidopsis MIKC MADS proteins in which predicted interaction motifs occur for two different motif groups: motifs that are located close to the intron/exon border (<3 amino acids distance, red) occur on average in a few proteins only, and motifs that are located far away from the border (> = 3 amino acids distance, green) occur in many proteins.
Mentions: Interestingly, the interaction motifs in the ‘hotspot region’ at the junction between MADS and I domain overlap an intron/exon boundary. This provides a plausible evolutionary mechanism to generate protein interaction diversity by shifting these intron/exon boundaries after duplications or via alternative splicing (Figure 5). Indeed the above mentioned cases where indels modify interaction motifs in duplicated proteins occur often in the MADS domain protein ‘hotspot region’, in which interaction motifs overlap an intron/exon boundary. An example of a change in interaction pattern via ‘splicing out’ of a predicted interaction motif is observed in a recently identified SVP splicing variant (named SVP3; Accession: EU078686; Figure 5). SVP3 lost the interaction motif found in the hotspot region of the fully spliced SVP protein (SVP1) leading to a large loss of protein interaction partners (Figure 5; Table 1; Figure S2). Additional discussion is provided in the Supplementary information (Text S1, Figure S1), where we also provide an analysis of the distance of predicted interaction motifs from intron/exon boundaries. Based on these findings we hypothesize that shifting intron/exon borders plays a role in neo-functionalization of plant MADS domain transcription factors by direct changing of dimerization capacity (Figure 5). Note that, at least in the above-mentioned SVP case, this mechanism seems to allow the duplicate to optimize in one specific interaction and avoid conflict with the original copy, by deleting other common interactions.

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