A universal code for RNA recognition by PUF proteins.

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.

[1]  C. Cheong,et al.  Engineering RNA sequence specificity of Pumilio repeats , 2006, Proceedings of the National Academy of Sciences.

[2]  M. Wickens,et al.  Chapter 14. Analysis of RNA-protein interactions using a yeast three-hybrid system. , 2008, Methods in enzymology.

[3]  M. Wickens,et al.  A three-hybrid system to detect RNA-protein interactions in vivo. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[4]  D. Larson,et al.  Single-RNA counting reveals alternative modes of gene expression in yeast , 2008, Nature Structural &Molecular Biology.

[5]  K. Oparka,et al.  Live-cell imaging of viral RNA genomes using a Pumilio-based reporter. , 2009, The Plant journal : for cell and molecular biology.

[6]  A. Aggarwal,et al.  Structure of Pumilio Reveals Similarity between RNA and Peptide Binding Motifs , 2001, Cell.

[7]  T. Glisovic,et al.  RNA‐binding proteins and post‐transcriptional gene regulation , 2008, FEBS letters.

[8]  R. Lehmann,et al.  The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. , 1997, RNA.

[9]  Aleksandra Filipovska,et al.  Building a Parallel Metabolism within the Cell. , 2008, ACS chemical biology.

[10]  Deepak T Nair,et al.  Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity. , 2008, Structure.

[11]  Marvin Wickens,et al.  RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening. , 2005, RNA.

[12]  R. D. Gietz,et al.  Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. , 2002, Methods in enzymology.

[13]  P. Brown,et al.  Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast , 2004, PLoS biology.

[14]  Gabriele Varani,et al.  RNA is rarely at a loss for companions; as soon as RNA , 2008 .

[15]  T. Ito,et al.  Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Farren J. Isaacs,et al.  Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.

[17]  R. Elkon,et al.  A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility , 2010, Nature Cell Biology.

[18]  T. Lithgow,et al.  PUF proteins: repression, activation and mRNA localization. , 2011, Trends in cell biology.

[19]  Phillip D. Zamore,et al.  Modular Recognition of RNA by a Human Pumilio-Homology Domain , 2002, Cell.

[20]  Farren J. Isaacs,et al.  RNA synthetic biology , 2006, Nature Biotechnology.

[21]  Daniel St Johnston,et al.  Moving messages: the intracellular localization of mRNAs , 2005, Nature Reviews Molecular Cell Biology.

[22]  J. Chin,et al.  A network of orthogonal ribosome·mRNA pairs , 2005, Nature chemical biology.

[23]  Yoshio Umezawa,et al.  Imaging dynamics of endogenous mitochondrial RNA in single living cells , 2007, Nature Methods.

[24]  M. Wickens,et al.  A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs , 2009, Proceedings of the National Academy of Sciences.

[25]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[26]  P. Zamore,et al.  Crystal structure of a Pumilio homology domain. , 2001, Molecular cell.

[27]  Marvin Wickens,et al.  Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein , 2009, Proceedings of the National Academy of Sciences.

[28]  Frédéric H.-T. Allain,et al.  Sequence-specific binding of single-stranded RNA: is there a code for recognition? , 2006, Nucleic acids research.

[29]  L. Cassiday,et al.  In vivo recognition of an RNA aptamer by its transcription factor target. , 2001, Biochemistry.

[30]  Yang Wang,et al.  Engineering splicing factors with designed specificities , 2009, Nature Methods.