The domains of polypyrimidine tract binding protein have distinct RNA structural preferences.
PTB (polypyrimidine tract binding protein) participates in cellular regulatory functions in the nucleus and the cytoplasm. It binds to internal ribosome entry sites to facilitate their use in cap-independent translation. It binds to polypyrimidine tracts in pre-mRNA introns to repress inclusion of exons. It binds to the 3' untranslated regions of mRNAs to stabilize the message. These RNAs have various structures, yet PTB binds to all of them. Here, RNAs with structured or unstructured polypyrimidine tracts are bound to the full-length PTB1 protein and two protein subdomains, each containing two RNA recognition motifs. Hairpin loops from c-src and GABAA gamma2 pre-mRNAs and from the 3' terminus of hepatitis C virus (HCV) were compared to a single-stranded polypyrimidine tract from GABAA gamma2 pre-mRNA. We conclude that PTB1 RNA binding function is modular: the N-terminal RRMs preferentially bind to short (U/C) tracts displayed in loops, while the RRM3-RRM4 complex preferentially binds to longer flexible RNA sequences. Since it can bind to short and long polypyrimidine tracts, structured or single-stranded, PTB takes on the role of a versatile adaptor protein that facilitates formation of RNA-protein regulatory complexes.
Clerte
Caroline
C
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Hall
Kathleen B
KB
D024202:Electrophoretic Mobility Shift Assay; D005454:Fluorescence Polarization; D016174:Hepacivirus / Q000235:genetics; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation / Q000502:physiology; D009690:Nucleic Acid Conformation; D038941:Polypyrimidine Tract-Binding Protein / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding / Q000502:physiology; D054730:Protein Interaction Domains and Motifs / Q000502:physiology*; D016392:Proto-Oncogene Proteins pp60(c-src) / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D011963:Receptors, GABA-A / Q000235:genetics; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid / Q000502:physiology; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics
C546279:GABRG2 protein, human; D034441:Heterogeneous-Nuclear Ribonucleoproteins; C450006:PTBP1 protein, human; D012333:RNA, Messenger; D011963:Receptors, GABA-A; D011994:Recombinant Proteins; D038621:Regulatory Sequences, Ribonucleic Acid; D054334:Viral Regulatory and Accessory Proteins; D038941:Polypyrimidine Tract-Binding Protein; D016392:Proto-Oncogene Proteins pp60(c-src)