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Literature DB >> 21572425

A universal code for RNA recognition by PUF proteins.

Aleksandra Filipovska¹, Muhammad F M Razif, Karoline K A Nygård, Oliver Rackham.

Abstract

The design of proteins that can bind any RNA sequence of interest has many potential biological and medical applications. Here we have expanded the recognition of Pumilio and FBF homology protein (PUF) repeats beyond adenine, guanine and uracil and evolved them to specifically bind cytosine. These repeat sequences can be used to create PUF domains capable of selectively binding RNA targets of diverse sequence and structure.

Entities: Chemical Gene

Mesh：

Substances：

Year: 2011 PMID： 21572425 DOI： 10.1038/nchembio.577

Source DB: PubMed Journal: Nat Chem Biol ISSN： 1552-4450 Impact factor: 15.040

25 in total

1. Structure of Pumilio reveals similarity between RNA and peptide binding motifs.

Authors: T A Edwards; S E Pyle; R P Wharton; A K Aggarwal
Journal: Cell Date: 2001-04-20 Impact factor: 41.582

2. Engineering RNA sequence specificity of Pumilio repeats.

Authors: Cheom-Gil Cheong; Traci M Tanaka Hall
Journal: Proc Natl Acad Sci U S A Date: 2006-09-05 Impact factor: 11.205

3. Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

Authors: Yogesh K Gupta; Deepak T Nair; Robin P Wharton; Aneel K Aggarwal
Journal: Structure Date: 2008-03-06 Impact factor: 5.006

4. Building a Parallel Metabolism within the Cell.

Authors: Aleksandra Filipovska; Oliver Rackham
Journal: ACS Chem Biol Date: 2008-01-04 Impact factor: 5.100

5. A three-hybrid system to detect RNA-protein interactions in vivo.

Authors: D J SenGupta; B Zhang; B Kraemer; P Pochart; S Fields; M Wickens
Journal: Proc Natl Acad Sci U S A Date: 1996-08-06 Impact factor: 11.205

6. A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility.

Authors: Martijn Kedde; Marieke van Kouwenhove; Wilbert Zwart; Joachim A F Oude Vrielink; Ran Elkon; Reuven Agami
Journal: Nat Cell Biol Date: 2010-09-05 Impact factor: 28.824

7. Single-RNA counting reveals alternative modes of gene expression in yeast.

Authors: Daniel Zenklusen; Daniel R Larson; Robert H Singer
Journal: Nat Struct Mol Biol Date: 2008-11-16 Impact factor: 15.369

Review 8. Sequence-specific binding of single-stranded RNA: is there a code for recognition?

Authors: Sigrid D Auweter; Florian C Oberstrass; Frédéric H-T Allain
Journal: Nucleic Acids Res Date: 2006-09-18 Impact factor: 16.971

9. Live-cell imaging of viral RNA genomes using a Pumilio-based reporter.

Authors: Jens Tilsner; Olga Linnik; Nynne M Christensen; Karen Bell; Ian M Roberts; Christophe Lacomme; Karl J Oparka
Journal: Plant J Date: 2008-11-17 Impact factor: 6.417

Review 10. RNA-binding proteins and post-transcriptional gene regulation.

Authors: Tina Glisovic; Jennifer L Bachorik; Jeongsik Yong; Gideon Dreyfuss
Journal: FEBS Lett Date: 2008-03-13 Impact factor: 4.124

69 in total

Review 1. Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.

Authors: Bram Stynen; Hélène Tournu; Jan Tavernier; Patrick Van Dijck
Journal: Microbiol Mol Biol Rev Date: 2012-06 Impact factor: 11.056

A universal code for RNA recognition by PUF proteins.

1. Structure of Pumilio reveals similarity between RNA and peptide binding motifs.

2. Engineering RNA sequence specificity of Pumilio repeats.

3. Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

4. Building a Parallel Metabolism within the Cell.

5. A three-hybrid system to detect RNA-protein interactions in vivo.

6. A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility.

7. Single-RNA counting reveals alternative modes of gene expression in yeast.

Review 8. Sequence-specific binding of single-stranded RNA: is there a code for recognition?

9. Live-cell imaging of viral RNA genomes using a Pumilio-based reporter.

Review 10. RNA-binding proteins and post-transcriptional gene regulation.

Review 1. Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.

2. From cis-regulatory elements to complex RNPs and back.

3. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.

4. The dataset for protein-RNA binding affinity.

5. How a CCA sequence protects mature tRNAs and tRNA precursors from action of the processing enzyme RNase BN/RNase Z.

6. Structural basis for RNA recognition by a dimeric PPR-protein complex.

7. Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.

8. Enzymatic fabrication of high-density RNA arrays.

9. Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells.

10. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts.