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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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Combining predicted protein-protein interaction motifs and modeled protein structures.(A) Modeled dimer for the Arabidopsis MADS domain protein SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). Blue indicates the DNA binding helix (in which no protein-protein interaction motifs are present). Residues indicated in spacefill (Ala57, Asn60 and Met61) are part of an experimentally validated interaction motif in the so-called ‘hotspot region’ (see text for details). (B) Crystal structure (PDB 1n6j) of human MADS domain protein MEF2 (grey) in complex with Cabin1 (red). Cabin1 contacts MEF2 via Met62 and a few other amino acid residues. MEF2 Met62 is the equivalent of Met61 in SOC1, with both amino acid residues having comparable positions in the structure. The residues of Cabin1 that contact Met62 (Ser101, Gly104 and Ile106) are shown in red spacefill. Based on the MEF2-Cabin1 structure we hypothesize a similar kind of binding of the α-helix-forming K-box from a SOC1 interacting MADS domain protein on top of the SOC1 MADS/I domain. (C) The black box indicates the predicted interaction motif in the ‘hotspot region’ of the SOC1 protein. The predicted complementary interaction motif (red box) is located in the K-box domain of the MADS domain protein interacting with SOC1.
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pcbi-1001017-g001: Combining predicted protein-protein interaction motifs and modeled protein structures.(A) Modeled dimer for the Arabidopsis MADS domain protein SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). Blue indicates the DNA binding helix (in which no protein-protein interaction motifs are present). Residues indicated in spacefill (Ala57, Asn60 and Met61) are part of an experimentally validated interaction motif in the so-called ‘hotspot region’ (see text for details). (B) Crystal structure (PDB 1n6j) of human MADS domain protein MEF2 (grey) in complex with Cabin1 (red). Cabin1 contacts MEF2 via Met62 and a few other amino acid residues. MEF2 Met62 is the equivalent of Met61 in SOC1, with both amino acid residues having comparable positions in the structure. The residues of Cabin1 that contact Met62 (Ser101, Gly104 and Ile106) are shown in red spacefill. Based on the MEF2-Cabin1 structure we hypothesize a similar kind of binding of the α-helix-forming K-box from a SOC1 interacting MADS domain protein on top of the SOC1 MADS/I domain. (C) The black box indicates the predicted interaction motif in the ‘hotspot region’ of the SOC1 protein. The predicted complementary interaction motif (red box) is located in the K-box domain of the MADS domain protein interacting with SOC1.

Mentions: For each protein the resulting predicted protein-protein interaction motifs from “ara_new” are given in Table S1. Motifs were found in all the different domains (MADS, I, K and C), but occurred most frequently at the border between the MADS and I-domain, in line with the proposed role of the I-domain in determining dimerization specificity [28], [29], [45]. This ‘hotspot’ region is homologous to a region in the human MADS domain protein Myocyte Enhancer Factor-2 (MEF2) [46] that interacts with a helix of the Cabin1 protein (Figure 1). The motif that is complementary to most of the motifs in the MIKC MADS hotspot region is found in the K-box of the interacting proteins, a domain that is predicted to form α-helices [47]–[49] comparable to Cabin1. This data suggests a specific mode of interaction between the I-region of plant MADS proteins and the K-domain of their interaction partners.


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)

Combining predicted protein-protein interaction motifs and modeled protein structures.(A) Modeled dimer for the Arabidopsis MADS domain protein SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). Blue indicates the DNA binding helix (in which no protein-protein interaction motifs are present). Residues indicated in spacefill (Ala57, Asn60 and Met61) are part of an experimentally validated interaction motif in the so-called ‘hotspot region’ (see text for details). (B) Crystal structure (PDB 1n6j) of human MADS domain protein MEF2 (grey) in complex with Cabin1 (red). Cabin1 contacts MEF2 via Met62 and a few other amino acid residues. MEF2 Met62 is the equivalent of Met61 in SOC1, with both amino acid residues having comparable positions in the structure. The residues of Cabin1 that contact Met62 (Ser101, Gly104 and Ile106) are shown in red spacefill. Based on the MEF2-Cabin1 structure we hypothesize a similar kind of binding of the α-helix-forming K-box from a SOC1 interacting MADS domain protein on top of the SOC1 MADS/I domain. (C) The black box indicates the predicted interaction motif in the ‘hotspot region’ of the SOC1 protein. The predicted complementary interaction motif (red box) is located in the K-box domain of the MADS domain protein interacting with SOC1.
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Related In: Results  -  Collection

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pcbi-1001017-g001: Combining predicted protein-protein interaction motifs and modeled protein structures.(A) Modeled dimer for the Arabidopsis MADS domain protein SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). Blue indicates the DNA binding helix (in which no protein-protein interaction motifs are present). Residues indicated in spacefill (Ala57, Asn60 and Met61) are part of an experimentally validated interaction motif in the so-called ‘hotspot region’ (see text for details). (B) Crystal structure (PDB 1n6j) of human MADS domain protein MEF2 (grey) in complex with Cabin1 (red). Cabin1 contacts MEF2 via Met62 and a few other amino acid residues. MEF2 Met62 is the equivalent of Met61 in SOC1, with both amino acid residues having comparable positions in the structure. The residues of Cabin1 that contact Met62 (Ser101, Gly104 and Ile106) are shown in red spacefill. Based on the MEF2-Cabin1 structure we hypothesize a similar kind of binding of the α-helix-forming K-box from a SOC1 interacting MADS domain protein on top of the SOC1 MADS/I domain. (C) The black box indicates the predicted interaction motif in the ‘hotspot region’ of the SOC1 protein. The predicted complementary interaction motif (red box) is located in the K-box domain of the MADS domain protein interacting with SOC1.
Mentions: For each protein the resulting predicted protein-protein interaction motifs from “ara_new” are given in Table S1. Motifs were found in all the different domains (MADS, I, K and C), but occurred most frequently at the border between the MADS and I-domain, in line with the proposed role of the I-domain in determining dimerization specificity [28], [29], [45]. This ‘hotspot’ region is homologous to a region in the human MADS domain protein Myocyte Enhancer Factor-2 (MEF2) [46] that interacts with a helix of the Cabin1 protein (Figure 1). The motif that is complementary to most of the motifs in the MIKC MADS hotspot region is found in the K-box of the interacting proteins, a domain that is predicted to form α-helices [47]–[49] comparable to Cabin1. This data suggests a specific mode of interaction between the I-region of plant MADS proteins and the K-domain of their interaction partners.

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