Binding specificity and mRNA targets of a <i>C. elegans</i> PUF protein, FBF-1

Bernstein, David; Hook, Brad; Hajarnavis, Ashwin; Opperman, Laura; Wickens, Marvin

doi:10.1261/rna.7255805

Cited by 125 publications

(161 citation statements)

References 32 publications

(71 reference statements)

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“…A crystal structure of the RNA-binding domain of FBF-2 in complex with a 9-nt consensus FBF binding element (FBE), 5Ј-UGUACUAUA-3Ј (20,28), was determined by single wavelength anomalous diffraction (SAD) and refined to a resolution of 2.2 Å. The initial experimental electron density map revealed density for all 9 RNA bases [supporting information (SI) Fig.…”

Section: Resultsmentioning

confidence: 99%

“…S2). The ninth position is not well conserved in natural targets, but RNA selections reveal a preference for A (28). In the FBF-2 structures, the ninth base stacks with Y245 of repeat 2 and is recognized by C204 or E208 from repeat 1, depending on the identity of the base (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The core FBF recognition sequence begins with a UGU triplet, as do all validated PUF target sequences. The optimal binding site is 5Ј-UGURNNAUA-3Ј (R, purine; N, any base; see Results) (28). PUF-8, a close relative in C. elegans to PUMILIO, recognizes a core 8-nt sequence (20), 5Ј-UGUANAUA-3Ј (4,(30)(31)(32), the same as that seen by PUM1 (30).…”

mentioning

confidence: 82%

“…FBF is required for maintenance of germline stem cells, a conserved function of PUF proteins (1). FBF maintains stem cells by repressing the expression of differentiation regulators, including gld-1, fog-1, lip-1, and mpk-1 (28). In addition, FBF regulates the switch from spermatogenesis to oogenesis by repressing fem-3 mRNA (8).…”

mentioning

confidence: 99%

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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.

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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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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 82%

mentioning

confidence: 99%

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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.

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109

150

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“…32 Individual target RNAs have been reported for specific Puf proteins; e.g., hb, cyclin B, HO, fem-3, COX17 and gld-1 mRNA. 33 In contrast to these reports, genome-wide RNA immunoprecipitation (RIP)-coupled microarray analyses showed that a single Puf protein is able to bind to multiple target RNAs. 23,34 For example, each of the five Puf proteins in yeast binds different subsets of mRNAs.…”

Section: Target Rnas For Pumilio Proteinsmentioning

confidence: 95%

Pumilio Puf domain RNA-binding proteins in Arabidopsis

Abbasi

Park

Choi

2011

Plant Signaling & Behavior

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Caenorhabditis elegans DLC‐1 associates with ribonucleoprotein complexes to promote mRNA regulation

2018

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Ribonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here, we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the C. elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs associated with oogenesis. Removal of DLC-1 affects expression of its targets expressed in the oocytes, meg-1 and meg-3. We propose that DLC-1 acts as a cofactor for multiple ribonucleoprotein complexes, including the ones regulating gene expression during oogenesis.

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

Cited by 125 publications

References 32 publications

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

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

Pumilio Puf domain RNA-binding proteins in Arabidopsis

Caenorhabditis elegans DLC‐1 associates with ribonucleoprotein complexes to promote mRNA regulation

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