title: The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.
abstract: Piwi-interacting RNAs (piRNAs) are small noncoding RNAs expressed in the germline of animals. They associate with Argonaute proteins of the Piwi subfamily, forming ribonucleoprotein complexes that are involved in maintaining genome integrity. The N-terminal region of some Piwi proteins contains symmetrically dimethylated arginines. This modification is thought to enable recruitment of Tudor domain-containing proteins (TDRDs), which might serve as platforms mediating interactions between various proteins in the piRNA pathway. We measured the binding affinity of the four individual extended Tudor domains (TDs) of murine TDRD1 protein for three different methylarginine-containing peptides from murine Piwi protein MILI. The results show a preference of TD2 and TD3 for consecutive MILI peptides, whereas TD4 and TD1 have, respectively, lower and very weak affinity for any peptide. The affinity of TD1 for methylarginine peptides can be restored by a single-point mutation back to the consensus aromatic cage sequence. These observations were confirmed by pull-down experiments with endogenous Piwi and Piwi-associated proteins. The crystal structure of TD3 bound to a methylated MILI peptide shows an unexpected orientation of the bound peptide, with additional contacts of nonmethylated residues being made outside of the aromatic cage, consistent with solution NMR titration experiments. Finally, the molecular envelope of the four tandem Tudor domains of TDRD1, derived from small angle scattering data, reveals a flexible, elongated shape for the protein. Overall, the results show that TDRD1 can accommodate different peptides from different proteins, and can therefore act as a scaffold protein for complex assembly in the piRNA pathway.
authors.affiliation: European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France.
authors.forename: Nikolas
authors.initials: N
authors.lastname: Mathioudakis
authors.forename: Andres
authors.initials: A
authors.lastname: Palencia
authors.forename: Jan
authors.initials: J
authors.lastname: Kadlec
authors.forename: Adam
authors.initials: A
authors.lastname: Round
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Tripsianes
authors.forename: Michael
authors.initials: M
authors.lastname: Sattler
authors.forename: Ramesh S
authors.initials: RS
authors.lastname: Pillai
authors.forename: Stephen
authors.initials: S
authors.lastname: Cusack
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D060565:Argonaute Proteins / Q000737:chemistry*; D001665:Binding Sites; D018797:Cell Cycle Proteins; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D034741:RNA, Small Interfering / Q000096:biosynthesis*; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry*; D053838:Scattering, Small Angle; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic
chemical_list: D060565:Argonaute Proteins; D018797:Cell Cycle Proteins; D010446:Peptide Fragments; C448521:Piwil2 protein, mouse; D034741:RNA, Small Interfering; D017411:Ribonucleoproteins, Small Nuclear; C488681:Tdrd1 protein, mouse