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Bicc1 Polymerization Regulates the Localization and Silencing of Bound mRNA.

Rothé B, Leal-Esteban L, Bernet F, Urfer S, Doerr N, Weimbs T, Iwaszkiewicz J, Constam DB - Mol. Cell. Biol. (2015)

Bottom Line: In addition, defective polymerization decreases Bicc1 stability and thus indirectly attenuates inhibition of Dishevelled 2 in the Wnt/β-catenin pathway.Importantly, aberrant C-terminal extension of the SAM domain in bpk mutant Bicc1 phenocopied these defects.We conclude that polymerization is a novel disease-relevant mechanism both to stabilize Bicc1 and to present associated mRNAs in specific silencing platforms.

View Article: PubMed Central - PubMed

Affiliation: Ecole Polytechnique Fédérale de Lausanne (EPFL), SV ISREC, Lausanne, Switzerland.

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Molecular modeling of a Bicc1 SAM polymer. (A) ClustalW alignment of mouse (Mus musculus) Bicc1 (mBicc1) and human (Homo sapiens) DGKδ1 (hDGKδ1) SAM domains. The X-ray structure of dimeric DGKδ1 SAM (PDB accession number 3BQ7) served as the template to model the Bicc1 SAM dimer. The two SAM domains share 31% identity and 54% similarity. Predicted α helices are framed. Residues of the ML surface (red), residues from the EH surface (blue), and hydrophobic residues (underlined) are highlighted. Dark and light gray shading corresponds to identical and similar amino acids, respectively, between Bicc1 and the DGKδ1 template. (B) Dimeric Bicc1 SAM model obtained using MODELLER (v9.5) software. The α helix numbers and the side chains of the residues involved in the interface are displayed. (C to E) Magnified views of the main interacting patches in the predicted Bicc1 SAM dimer interface. Acidic and basic residues are displayed in red and blue, respectively. (F) Model of a Bicc1 SAM polymer of 24 units in surface representation. The NH2 terminus and the COOH terminus of each SAM domain are displayed in green and purple, respectively. (G) Model of the Bicc1 KH domain region in surface representation. Models for individual KH domains were obtained by homology modeling using the SWISS-MODEL work space (48) and templates consisting of the structures with PDB accession numbers 1VIG (KH1), 2CTM (KH2), 1WVN (KH3), and 3N89 (KHL1 and -2). Individual KH domains were then superimposed with their homologous domain in the X-ray structure of ceGLD-3 KH domains (PDB accession number 3N89) (58). The KH domains harboring the GXXG signatures for RNA binding are highlighted in color. Their putative RNA-binding surfaces are darkened, and the identity of their GXXG signature sequence is given in parentheses. The KH-like domains (KHL1 and -2) are displayed in gray. (H) Diagram of a transversal section through a polymer of full-length Bicc1. The SAM polymer is located at the center and displays other Bicc1 domains at its periphery. A schematic representation was used for the other domains. C-ter domain, C-terminal domain. (I) Diagram in longitudinal view of Bicc1 KH domains distributed along the surface of the central SAM polymer.
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Figure 3: Molecular modeling of a Bicc1 SAM polymer. (A) ClustalW alignment of mouse (Mus musculus) Bicc1 (mBicc1) and human (Homo sapiens) DGKδ1 (hDGKδ1) SAM domains. The X-ray structure of dimeric DGKδ1 SAM (PDB accession number 3BQ7) served as the template to model the Bicc1 SAM dimer. The two SAM domains share 31% identity and 54% similarity. Predicted α helices are framed. Residues of the ML surface (red), residues from the EH surface (blue), and hydrophobic residues (underlined) are highlighted. Dark and light gray shading corresponds to identical and similar amino acids, respectively, between Bicc1 and the DGKδ1 template. (B) Dimeric Bicc1 SAM model obtained using MODELLER (v9.5) software. The α helix numbers and the side chains of the residues involved in the interface are displayed. (C to E) Magnified views of the main interacting patches in the predicted Bicc1 SAM dimer interface. Acidic and basic residues are displayed in red and blue, respectively. (F) Model of a Bicc1 SAM polymer of 24 units in surface representation. The NH2 terminus and the COOH terminus of each SAM domain are displayed in green and purple, respectively. (G) Model of the Bicc1 KH domain region in surface representation. Models for individual KH domains were obtained by homology modeling using the SWISS-MODEL work space (48) and templates consisting of the structures with PDB accession numbers 1VIG (KH1), 2CTM (KH2), 1WVN (KH3), and 3N89 (KHL1 and -2). Individual KH domains were then superimposed with their homologous domain in the X-ray structure of ceGLD-3 KH domains (PDB accession number 3N89) (58). The KH domains harboring the GXXG signatures for RNA binding are highlighted in color. Their putative RNA-binding surfaces are darkened, and the identity of their GXXG signature sequence is given in parentheses. The KH-like domains (KHL1 and -2) are displayed in gray. (H) Diagram of a transversal section through a polymer of full-length Bicc1. The SAM polymer is located at the center and displays other Bicc1 domains at its periphery. A schematic representation was used for the other domains. C-ter domain, C-terminal domain. (I) Diagram in longitudinal view of Bicc1 KH domains distributed along the surface of the central SAM polymer.

Mentions: Bicc1 is localized in cytoplasmic foci by its SAM domain independently of the RNA-binding KH domains (35). Certain SAM domains can form dimers or polymeric structures (57), and a polymer of the human Bicc1 SAM domain fused to GFP has been observed in vitro by electron microscopy (EM) (42). To test whether SAM polymerization is responsible for Bicc1 clustering, we searched for mutations that specifically disrupt polymerization. Since structure data for Bicc1 or its SAM domain are currently unavailable, mutations were designed on the basis of homology modeling, where the known structure of a related protein serves as a template. Among the available templates, we selected the SAM domain dimer of the diacylglycerol kinase δ1 (DGKδ1) E35G (PDB accession number 3BQ7) because it shares the highest sequence similarity (54%) and identity (31%) with the Bicc1 SAM domain (Fig. 3A) and can form head-to-tail polymers (47). A model of dimeric Bicc1 SAM obtained after energy minimization revealed a common globular fold of five α helices, with two SAM subunits being docked to one another at characteristic ML and EH surfaces (Fig. 3B) (40). Residues involved in the dimerization of the DGKδ1 SAM are conserved or replaced by similar amino acids in the Bicc1 SAM domain (highlighted in Fig. 3A). At the Bicc1 SAM-SAM interface, 4 negatively charged amino acids on the ML surface (Glu900, Asp902, Asp913, Glu916) and 5 positively charged amino acids from the EH surface (Lys891, Lys915, Arg925, Arg926, Lys927) form strongly polarized electrostatic networks in two independent regions of contact (Fig. 3C and D; see also Fig. S5 in the supplemental material). In addition, residue Phe922 from the EH surface reaches into a hydrophobic pocket of the ML surface comprising Phe896, Ile901, Leu909, and Leu917 (Fig. 3E).


Bicc1 Polymerization Regulates the Localization and Silencing of Bound mRNA.

Rothé B, Leal-Esteban L, Bernet F, Urfer S, Doerr N, Weimbs T, Iwaszkiewicz J, Constam DB - Mol. Cell. Biol. (2015)

Molecular modeling of a Bicc1 SAM polymer. (A) ClustalW alignment of mouse (Mus musculus) Bicc1 (mBicc1) and human (Homo sapiens) DGKδ1 (hDGKδ1) SAM domains. The X-ray structure of dimeric DGKδ1 SAM (PDB accession number 3BQ7) served as the template to model the Bicc1 SAM dimer. The two SAM domains share 31% identity and 54% similarity. Predicted α helices are framed. Residues of the ML surface (red), residues from the EH surface (blue), and hydrophobic residues (underlined) are highlighted. Dark and light gray shading corresponds to identical and similar amino acids, respectively, between Bicc1 and the DGKδ1 template. (B) Dimeric Bicc1 SAM model obtained using MODELLER (v9.5) software. The α helix numbers and the side chains of the residues involved in the interface are displayed. (C to E) Magnified views of the main interacting patches in the predicted Bicc1 SAM dimer interface. Acidic and basic residues are displayed in red and blue, respectively. (F) Model of a Bicc1 SAM polymer of 24 units in surface representation. The NH2 terminus and the COOH terminus of each SAM domain are displayed in green and purple, respectively. (G) Model of the Bicc1 KH domain region in surface representation. Models for individual KH domains were obtained by homology modeling using the SWISS-MODEL work space (48) and templates consisting of the structures with PDB accession numbers 1VIG (KH1), 2CTM (KH2), 1WVN (KH3), and 3N89 (KHL1 and -2). Individual KH domains were then superimposed with their homologous domain in the X-ray structure of ceGLD-3 KH domains (PDB accession number 3N89) (58). The KH domains harboring the GXXG signatures for RNA binding are highlighted in color. Their putative RNA-binding surfaces are darkened, and the identity of their GXXG signature sequence is given in parentheses. The KH-like domains (KHL1 and -2) are displayed in gray. (H) Diagram of a transversal section through a polymer of full-length Bicc1. The SAM polymer is located at the center and displays other Bicc1 domains at its periphery. A schematic representation was used for the other domains. C-ter domain, C-terminal domain. (I) Diagram in longitudinal view of Bicc1 KH domains distributed along the surface of the central SAM polymer.
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Figure 3: Molecular modeling of a Bicc1 SAM polymer. (A) ClustalW alignment of mouse (Mus musculus) Bicc1 (mBicc1) and human (Homo sapiens) DGKδ1 (hDGKδ1) SAM domains. The X-ray structure of dimeric DGKδ1 SAM (PDB accession number 3BQ7) served as the template to model the Bicc1 SAM dimer. The two SAM domains share 31% identity and 54% similarity. Predicted α helices are framed. Residues of the ML surface (red), residues from the EH surface (blue), and hydrophobic residues (underlined) are highlighted. Dark and light gray shading corresponds to identical and similar amino acids, respectively, between Bicc1 and the DGKδ1 template. (B) Dimeric Bicc1 SAM model obtained using MODELLER (v9.5) software. The α helix numbers and the side chains of the residues involved in the interface are displayed. (C to E) Magnified views of the main interacting patches in the predicted Bicc1 SAM dimer interface. Acidic and basic residues are displayed in red and blue, respectively. (F) Model of a Bicc1 SAM polymer of 24 units in surface representation. The NH2 terminus and the COOH terminus of each SAM domain are displayed in green and purple, respectively. (G) Model of the Bicc1 KH domain region in surface representation. Models for individual KH domains were obtained by homology modeling using the SWISS-MODEL work space (48) and templates consisting of the structures with PDB accession numbers 1VIG (KH1), 2CTM (KH2), 1WVN (KH3), and 3N89 (KHL1 and -2). Individual KH domains were then superimposed with their homologous domain in the X-ray structure of ceGLD-3 KH domains (PDB accession number 3N89) (58). The KH domains harboring the GXXG signatures for RNA binding are highlighted in color. Their putative RNA-binding surfaces are darkened, and the identity of their GXXG signature sequence is given in parentheses. The KH-like domains (KHL1 and -2) are displayed in gray. (H) Diagram of a transversal section through a polymer of full-length Bicc1. The SAM polymer is located at the center and displays other Bicc1 domains at its periphery. A schematic representation was used for the other domains. C-ter domain, C-terminal domain. (I) Diagram in longitudinal view of Bicc1 KH domains distributed along the surface of the central SAM polymer.
Mentions: Bicc1 is localized in cytoplasmic foci by its SAM domain independently of the RNA-binding KH domains (35). Certain SAM domains can form dimers or polymeric structures (57), and a polymer of the human Bicc1 SAM domain fused to GFP has been observed in vitro by electron microscopy (EM) (42). To test whether SAM polymerization is responsible for Bicc1 clustering, we searched for mutations that specifically disrupt polymerization. Since structure data for Bicc1 or its SAM domain are currently unavailable, mutations were designed on the basis of homology modeling, where the known structure of a related protein serves as a template. Among the available templates, we selected the SAM domain dimer of the diacylglycerol kinase δ1 (DGKδ1) E35G (PDB accession number 3BQ7) because it shares the highest sequence similarity (54%) and identity (31%) with the Bicc1 SAM domain (Fig. 3A) and can form head-to-tail polymers (47). A model of dimeric Bicc1 SAM obtained after energy minimization revealed a common globular fold of five α helices, with two SAM subunits being docked to one another at characteristic ML and EH surfaces (Fig. 3B) (40). Residues involved in the dimerization of the DGKδ1 SAM are conserved or replaced by similar amino acids in the Bicc1 SAM domain (highlighted in Fig. 3A). At the Bicc1 SAM-SAM interface, 4 negatively charged amino acids on the ML surface (Glu900, Asp902, Asp913, Glu916) and 5 positively charged amino acids from the EH surface (Lys891, Lys915, Arg925, Arg926, Lys927) form strongly polarized electrostatic networks in two independent regions of contact (Fig. 3C and D; see also Fig. S5 in the supplemental material). In addition, residue Phe922 from the EH surface reaches into a hydrophobic pocket of the ML surface comprising Phe896, Ile901, Leu909, and Leu917 (Fig. 3E).

Bottom Line: In addition, defective polymerization decreases Bicc1 stability and thus indirectly attenuates inhibition of Dishevelled 2 in the Wnt/β-catenin pathway.Importantly, aberrant C-terminal extension of the SAM domain in bpk mutant Bicc1 phenocopied these defects.We conclude that polymerization is a novel disease-relevant mechanism both to stabilize Bicc1 and to present associated mRNAs in specific silencing platforms.

View Article: PubMed Central - PubMed

Affiliation: Ecole Polytechnique Fédérale de Lausanne (EPFL), SV ISREC, Lausanne, Switzerland.

Show MeSH
Related in: MedlinePlus