Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast

Jackson, John S.; Houshmandi, Sean S.; Leban, Florencia Lopez; Olivas, Wendy M.

doi:10.1261/rna.7270204

Cited by 74 publications

(113 citation statements)

References 48 publications

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“…Cytosine at position Ϫ1 results in a modest 2-fold tighter binding versus uracil at that position. The tight binding for each site is consistent with in vivo experiments demonstrating delayed deadenylation and decay of the COX17 transcript when either of the binding sites was destroyed (12). * A Distinctive Binding Pocket in Puf3p.…”

Section: General Puf3psupporting

confidence: 73%

“…3A) (7,12,28,29). The C(Ϫ2)A double mutant was stabilized approximately 4-fold in the same cells (half-life Ϸ17 min).…”

Section: Regulation By Puf3p In Vivo Requiresmentioning

confidence: 96%

“…Loss of this single PUF protein impairs mitochondrial morphology and maintenance (9) and disrupts localization of its target mRNAs to the vicinity of mitochondria (10). Puf3p binds to and destabilizes COX17 mRNA, which encodes a copper metallochaperone involved in the biogenesis of the mitochondrial respiratory complex (7,11,12). Thus, by controlling a large battery of mRNAs, this single PUF protein is vital for regulation of the organelle.…”

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confidence: 99%

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A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

Zhu

Stumpf

Krahn

et al. 2009

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

115

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A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity. To do so, we explore the crystal structures of Puf3p complexes with 2 cognate RNAs. The key determinant of Puf3p specificity is an unusual interaction between a distinctive pocket of the protein with an RNA base outside the ''core'' PUF-binding site. That interaction dramatically affects binding affinity in vitro and is required for regulation in vivo. The Puf3p structures, combined with those of Puf4p in the same organism, illuminate the structural basis of natural PUF-RNA networks. Yeast Puf3p binds its own RNAs because they possess a ؊2C and is excluded from those of Puf4p which contain an additional nucleotide in the core-binding site.crystal structure ͉ RNA ͉ translational regulation

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Section: General Puf3psupporting

confidence: 73%

“…3A) (7,12,28,29). The C(Ϫ2)A double mutant was stabilized approximately 4-fold in the same cells (half-life Ϸ17 min).…”

Section: Regulation By Puf3p In Vivo Requiresmentioning

confidence: 96%

mentioning

confidence: 99%

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A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

Zhu

Stumpf

Krahn

et al. 2009

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

115

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“…This domain comprises 8 PUF repeats, flanked by pseudorepeats (8)(9)(10)(11). The PUF domain is sufficient to bind target mRNAs (8,10,12), recruit partner proteins (13)(14)(15)(16), and regulate mRNAs in vivo (2,17).…”

mentioning

confidence: 99%

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

Wang

Opperman

Wickens

et al. 2009

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

110

150

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Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4 -6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.crystal structure ͉ RNA ͉ translational regulation ͉ fem-3 binding factor ͉ base flipping

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“…This Puf repeat domain is sufficient not only for mRNA binding (Zamore et al 1997;Zhang et al 1997;Jackson et al 2004) but also for interacting with protein partners (Kraemer et al 1999;Sonada andWharton 1999, 2001;Luitjens et al 2000) and, at least in DmPum and the yeast Puf3p, for regulating mRNA metabolism (Wharton et al 1998;Jackson et al 2004). The crystal structures of the repeat domains of DmPum (Edwards et al 2001) and a human Puf protein (HsPum) (Wang et al 2001) are similar.…”

Section: Introductionmentioning

confidence: 99%

Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay

Houshmandi¹,

Olivas²

2005

RNA

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The eukaryotic Puf proteins regulate mRNA translation and degradation by binding the 3 0 untranslated regions of target mRNAs. Crystal structure analysis of a human Puf bound to RNA suggested a modular mode of binding, with specific amino acids within each of eight repeat domains contacting a single nucleotide of the target RNA. Here we study the mechanism by which the yeast Puf3p binds and stimulates the degradation of COX17 mRNA. Mutation of the predicted RNA-binding positions of Puf3p to those found in Puf5p demonstrated that a single amino acid change in Puf3p abolished detectable binding to COX17. Since this amino acid position in both Puf3p and Puf5p is predicted to contact an adenine in the respective target RNAs, the amino acid in Puf3p must play a more critical role in promoting COX17 interaction. In contrast, an amino acid change in the third repeat of Puf3p, which interacts with the only divergent nucleotide between the Puf3p and Puf5p targets, had no effect on binding COX17. These results argue that a simple set of rules cannot reliably link specific amino acid positions with target specificity. Each of these amino acid changes in Puf3p enhanced binding to the Puf5p target HO RNA, suggesting a different mode of binding to this target. Finally, we identified an outer surface loop that was dispensable for binding but was required to promote both rapid deadenylation and subsequent decapping of the COX17 mRNA, most likely as a point of protein-protein interactions.

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Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast

Cited by 74 publications

References 48 publications

A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

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

Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay

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