A Role for the Poly(A)-binding Protein Pab1p in PUF Protein-mediated Repression

Abstract

PUF proteins regulate translation and mRNA stability throughout eukaryotes. Using a cell-free translation assay, we examined the mechanisms of translational repression of PUF proteins in the budding yeast Saccharomyces cerevisiae. We demonstrate that the poly(A)-binding protein Pab1p is required for PUF-mediated translational repression for two distantly related PUF proteins: S. cerevisiae Puf5p and Caenorhabditis elegans FBF-2. Pab1p interacts with oligo(A) tracts in the HO 3-UTR, a target of Puf5p, to dramatically enhance the efficiency of Puf5p repression. Both the Pab1p ability to activate translation and interact with eukaryotic initiation factor 4G (eIF4G) were required to observe maximal repression by Puf5p. Repression was also more efficient when Pab1p was bound in close proximity to Puf5p. Puf5p may disrupt translation initiation by interfering with the interaction between Pab1p and eIF4G. Finally, we demonstrate two separable mechanisms of translational repression employed by Puf5p: a Pab1p-dependent mechanism and a Pab1p-independent mechanism.Regulation of messenger RNA (mRNA) is an important part of gene expression. Each mRNA contains instructions that determine where and when it will be expressed. Many of the instructions are contained in the untranslated regions (UTRs) 2 of the mRNA (1, 2). UTRs encode instructions for translation activation, repression, mRNA decay, or localization (3). The instructions take the form of primary sequences and structural elements that can be recognized by RNA-binding proteins (RBPs) and microRNAs (miRNAs). The combination of these factors assembled on each transcript determines the fate of each mRNA.PUF proteins are a family of RBPs that regulate the translation and stability of mRNAs to which they bind, typically by repressing their expression (4 -9). PUFs recognize elements that contain a conserved UGU sequence located in the 3Ј-UTR of target mRNAs (8, 10). PUF proteins often act as part of a larger regulatory complex, providing RNA binding specificity while other factors accomplish regulation (7,(11)(12)(13)(14).PUF proteins utilize two mechanisms to repress mRNA expression: destabilization and translational repression (8). Shortening of the poly(A) tail is the first step of mRNA decay in eukaryotes (15). In yeast, Puf5p interacts with Pop2p, a member of the Ccr4/Not deadenylase complex, facilitating deadenylation and decay of target mRNAs (11, 16). PUF-mediated recruitment of the Ccr4/Not complex has been demonstrated in Caenorhabditis elegans, Drosphila, and humans, suggesting that it is a conserved regulatory mechanism (11, 12).PUF proteins employ several different mechanisms to disrupt translation initiation. During the first step of initiation, the mRNA is circularized by the eIF4F complex, which then facilitates ribosome recruitment (17, 18). Circularization is achieved by eIF4G binding to both the cap-binding protein eIF4E and the poly(A)-binding protein PABP, bringing both ends of the mRNA in proximity (19). Drosophila Pumilio disrupts circularization by r...

The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation

“…We note that our attempts to detect association of eIF4G with Pum RBD have been unsuccessful. Supporting this model, Chritton and Wickens showed that the Pab1-eIF4G interaction is required for repression by yeast Puf5 in vitro (Chritton and Wickens 2011). As a result, Pumilio would disrupt the "closed loop" contacts between 5…”

“…Using a translationally active yeast extract, the pAbp ortholog, Pab1p, was shown to participate in translational inhibition by the RBD of yeast Puf5 (Chritton and Wickens 2011). In this same yeast extract, the RBD of C. elegans FBF also inhibited translation in a Pab1p-dependent manner (Chritton and Wickens 2011). In addition, pAbp colocalizes with PUFs in ribonucleoprotein granules in rat neurons (Vessey et al 2010).…”

“…8 further supports the importance of pAbp in PUF repression. Using a translationally active yeast extract, the pAbp ortholog, Pab1p, was shown to participate in translational inhibition by the RBD of yeast Puf5 (Chritton and Wickens 2011). In this same yeast extract, the RBD of C. elegans FBF also inhibited translation in a Pab1p-dependent manner (Chritton and Wickens 2011).…”

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

“…Perhaps the proximity of the GC-rich stem-loop to the poly(A) tail inhibits cooperative binding of Pab1 to the poly(A) tail and neighboring sequences. Because Pab1 can interact with sequences upstream of cleavage and polyadenylation sites (Simón and Séraphin, 2007; Chritton and Wickens, 2011), any reduction in single-stranded character at the 3′ ends of isoforms and/or poly(A) tails might result in reduced Pab1 binding. It is also possible that the GC-rich elements may be forming higher-order structures such as triple helices that shield the poly(A) tail (Mitton-Fry et al, 2010; Brown et al, 2012; Tycowski et al, 2012).…”

Differential Localization of the Two T. brucei Poly(A) Binding Proteins to the Nucleus and RNP Granules Suggests Binding to Distinct mRNA Pools

“…For example, PABPs are involved in both general mRNA metabolism, such as control of mRNA half-life and nonsense mediated decay (NMD) [3], [4], and in mRNA specific functions [5]. The latter includes the regulation of translation by binding to A-rich stretches in 5′ UTRs [6] or 3′ UTRs [7], [8], [9], including the 5′ UTR of its own mRNAs [10], [11], [12], [13], an involvement in miRNA induced silencing by binding to the miRISC complex [14], [15] and contributing to nuclear mRNA processing [16]. Similarly, eIF4E proteins can repress translation of individual mRNAs.…”