Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

Wang, Yeming; Opperman, Laura; Wickens, Marvin; Hall, Traci M. Tanaka

doi:10.1073/pnas.0812076106

Cited by 110 publications

(166 citation statements)

References 43 publications

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“…However, alanine substitutions in the stacking residues of repeats 1 and 5, as well as in the edge-on residues of repeats 1, 4, 5 and 8, allowed 10% or more β-gal activity. These data are consistent with interactions in the crystal structures of FBF-2/RNA complexes (30).…”

Section: Systematic Mutagenesis Reveals a Common Pattern Of Recognitionsupporting

confidence: 79%

“…The identity of the base present in each mutant is indicated immediately below the bars; the identity in WT is indicated below that. Amino acid side chains and bases in the FBF-2/FBE (C), Puf4p/4BE (F), and Puf3p/3BE (I) complexes are derived from the crystal structures (29,30,35). Green amino acid chains allowed ≥10% β-gal when mutated to alanine, and red side chains allowed <10% when mutated to alanine.…”

Section: Systematic Mutagenesis Reveals a Common Pattern Of Recognitionmentioning

confidence: 99%

“…Other PUFs require "extra" bases relative to human Pumilio; these are accommodated by "base flipping" (29)(30)(31). These bases do not contact the edge-on or stacking side chain but flip away from the protein instead.…”

mentioning

confidence: 99%

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Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

Valley¹,

Porter

Qiu

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved "two-handed" pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins.mRNA turnover | RNA regulation | translation | 3′UTR elements

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Section: Systematic Mutagenesis Reveals a Common Pattern Of Recognitionsupporting

confidence: 79%

Section: Systematic Mutagenesis Reveals a Common Pattern Of Recognitionmentioning

confidence: 99%

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Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

Valley¹,

Porter

Qiu

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…Although biochemical and structural studies of PUFs have shown that they interact with RNA in a modular manner, their diverse repeats make designing RNA-binding proteins free from context-dependent effects or with predictable binding affinities challenging. Furthermore, the structures of PUF proteins provide certain key limitations to their possible applications; their overall fold limits the number of repeats that can be assembled contiguously and the tendency for some bases of the target RNA to flip out from the RNA-binding surface can result in reduced RNA-binding specificity [35][36][37][38] . PPR proteins have a number of desirable features that make the development of their applications in biotechnology and synthetic biology quite appealing, now that a robust soluble and fully synthetic PPR module has been developed.…”

Section: Discussionmentioning

confidence: 99%

An artificial PPR scaffold for programmable RNA recognition

et al. 2014

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Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.

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“…23 The basis for this selectivity lies in the nucleotides at positions 4-6 of the target mRNA. 35 Further complicating the issue, Puf proteins can act alone or in combination with other Puf proteins or protein partners to recognize their target RNAs. 9,36-38…”

Section: Target Rnas For Pumilio Proteinsmentioning

confidence: 99%