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Literature DB >> 26874972

De-coding and re-coding RNA recognition by PUF and PPR repeat proteins.

Abstract

PUF and PPR proteins are two families of α-helical repeat proteins that recognize single-stranded RNA sequences. Both protein families hold promise as scaffolds for designed RNA-binding domains. A modular protein RNA recognition code was apparent from the first crystal structures of a PUF protein in complex with RNA, and recent studies continue to advance our understanding of natural PUF protein recognition (de-coding) and our ability to engineer specificity (re-coding). Degenerate recognition motifs make de-coding specificity of individual PPR proteins challenging. Nevertheless, re-coding PPR protein specificity using a consensus recognition code has been successful. Published by Elsevier Ltd.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
RNA-Binding Proteins
RNA

Year: 2016 PMID： 26874972 PMCID： PMC4757904 DOI： 10.1016/j.sbi.2016.01.010

Source DB: PubMed Journal: Curr Opin Struct Biol ISSN： 0959-440X Impact factor: 6.809

49 in total

1. Crystal structure of a Pumilio homology domain.

Authors: X Wang; P D Zamore; T M Hall
Journal: Mol Cell Date: 2001-04 Impact factor: 17.970

2. Modular recognition of RNA by a human pumilio-homology domain.

Authors: Xiaoqiang Wang; Juanita McLachlan; Phillip D Zamore; Traci M Tanaka Hall
Journal: Cell Date: 2002-08-23 Impact factor: 41.582

3. Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1.

Authors: David Bernstein; Brad Hook; Ashwin Hajarnavis; Laura Opperman; Marvin Wickens
Journal: RNA Date: 2005-04 Impact factor: 4.942

4. A single spacer nucleotide determines the specificities of two mRNA regulatory proteins.

Authors: Laura Opperman; Brad Hook; Mia DeFino; David S Bernstein; Marvin Wickens
Journal: Nat Struct Mol Biol Date: 2005-11 Impact factor: 15.369

5. 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

6. 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

7. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p.

Authors: Matthew T Miller; Joshua J Higgin; Traci M Tanaka Hall
Journal: Nat Struct Mol Biol Date: 2008-03-09 Impact factor: 15.369

8. Imaging dynamics of endogenous mitochondrial RNA in single living cells.

Authors: Takeaki Ozawa; Yutaka Natori; Moritoshi Sato; Yoshio Umezawa
Journal: Nat Methods Date: 2007-04-01 Impact factor: 28.547

9. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.

Authors: Claire Lurin; Charles Andrés; Sébastien Aubourg; Mohammed Bellaoui; Frédérique Bitton; Clémence Bruyère; Michel Caboche; Cédrig Debast; José Gualberto; Beate Hoffmann; Alain Lecharny; Monique Le Ret; Marie-Laure Martin-Magniette; Hakim Mireau; Nemo Peeters; Jean-Pierre Renou; Boris Szurek; Ludivine Taconnat; Ian Small
Journal: Plant Cell Date: 2004-07-21 Impact factor: 11.277

10. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.

Authors: André P Gerber; Daniel Herschlag; Patrick O Brown
Journal: PLoS Biol Date: 2004-03-16 Impact factor: 8.029

22 in total

1. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA.

Authors: Takamasa Teramoto; Kipchumba J Kaitany; Yoshimitsu Kakuta; Makoto Kimura; Carol A Fierke; Traci M Tanaka Hall
Journal: Nucleic Acids Res Date: 2020-12-02 Impact factor: 16.971

De-coding and re-coding RNA recognition by PUF and PPR repeat proteins.

1. Crystal structure of a Pumilio homology domain.

2. Modular recognition of RNA by a human pumilio-homology domain.

3. Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1.

4. A single spacer nucleotide determines the specificities of two mRNA regulatory proteins.

5. Engineering RNA sequence specificity of Pumilio repeats.

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

7. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p.

8. Imaging dynamics of endogenous mitochondrial RNA in single living cells.

9. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.

10. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast.

1. Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA.

2. Designer PPR Proteins as Tools to Explore RNA Binding in Vivo.

Review 3. Programmable RNA manipulation in living cells.

4. Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis.

5. Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins.

6. In silico evolution of nucleic acid-binding proteins from a nonfunctional scaffold.

7. Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans.

Review 8. The FASTK family of proteins: emerging regulators of mitochondrial RNA biology.

9. Structural basis for the specific recognition of 18S rRNA by APUM23.

10. CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.