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. 2009 Aug 28;35(4):479-89.
doi: 10.1016/j.molcel.2009.06.026.

Eukaryotic initiation factor 4a3 is a selenium-regulated RNA-binding protein that selectively inhibits selenocysteine incorporation

Michael E Budiman  1 , Jodi L Bubenik, Angela C Miniard, Lisa M Middleton, Carri A Gerber, Ayla Cash, Donna M Driscoll
Affiliations

Eukaryotic initiation factor 4a3 is a selenium-regulated RNA-binding protein that selectively inhibits selenocysteine incorporation

Michael E Budiman et al. Mol Cell. .

Abstract

The synthesis of selenoproteins requires the translational recoding of the UGA stop codon as selenocysteine. During selenium deficiency, there is a hierarchy of selenoprotein expression, with certain selenoproteins synthesized at the expense of others. The mechanism by which the limiting selenocysteine incorporation machinery is preferentially utilized to maintain the expression of essential selenoproteins has not been elucidated. Here we demonstrate that eukaryotic initiation factor 4a3 (eIF4a3) is involved in the translational control of a subset of selenoproteins. The interaction of eIF4a3 with the selenoprotein mRNA prevents the binding of SECIS binding protein 2, which is required for selenocysteine insertion, thereby inhibiting the synthesis of the selenoprotein. Furthermore, the expression of eIF4a3 is regulated in response to selenium. Based on knockdown and overexpression studies, eIF4a3 is necessary and sufficient to mediate selective translational repression in cells. Our results support a model in which eIF4a3 links selenium status with differential selenoprotein expression.

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Figures

Figure 1
Figure 1. Identification of a 48 kDa SECIS binding protein
(A) Schematic representation of the GPx1 and PHGPx SECIS elements. The SECIS Core, AAR motif and Internal Loop region are indicated. The location of the AAR motif determines whether the element is a type 1 SECIS (Apical Loop) or type 2 SECIS (Bulge). (B) Radiolabeled GPx1 or PHGPx SECIS probes (1 nM) were used with McArdle 7777 nuclear extract (50 μg) in UV-crosslinking assays. The 48 kDa protein that binds only to the GPx1 probe is indicated by the arrow. (C) Biotinylated GPx1 or PHGPx SECIS RNAs were incubated with McArdle 7777 nuclear extract. The bound proteins were eluted and analyzed by SDS-PAGE and Coomassie Blue-staining as described in Experimental Procedures. The arrow indicates the 48 kDa protein identified by LCMS.
Figure 2
Figure 2. eIF4a3 selectively interacts with the GPx1 SECIS
(A) Radiolabeled GPx1 or PHGPx SECIS RNAs were UV-crosslinked in the presence of varying amounts (0 to 400 ng) of recombinant rat eIF4a3. The arrow indicates the position of the crosslinked product. (B) Crosslinking of eIF4a3 to the radiolabeled GPx1 probe was competed with increasing concentrations (1 to 200 nM) of unlabeled GPx1 or PHGPx SECIS RNAs. (C) Quantification of the competition experiments. The IC50s were calculated as the concentration of RNA required to decrease the crosslinking signal by 50%. The data from 4 independent observations are represented as the mean +/− SD.
Figure 3
Figure 3. Selective inhibition of UGA recoding activity by eIF4a3
(A) Varying amounts of eIF4a3 (25 to 200 ng) were added to in vitro translation assays containing 100 ng of luc/UGA/GPx1, luc/UGA/PHGPx, or luc/UGU/GPx1 reporter mRNA. The luciferase results were expressed relative to reactions that were performed in the absence of eIF4a3. The data are represented as mean +/− SEM. (B) REMSA assay using the 32P-labeled GPx1 SECIS element, which was incubated with increasing amounts of eIF4a3 protein as indicated. The samples were then analyzed by native gel electrophoresis and autoradiography. Representative REMSA assays for the SelR, TR1, and PHGPx SECIS elements are shown in Supplementary Fig. 2. (C) Graph illustrating the apparent Kds of eIF4a3 for the GPx1, SelR, TR1, and PHGPx SECIS elements, which were calculated as the concentration of protein required to achieve 50% binding of the RNA. (D) Recoding assays were performed as described in (A) using reporter constructs containing the SelR and TR1 SECIS elements.
Figure 4
Figure 4. GPx1 SECIS-binding activities of eIF4a3 and SBP2 in vitro
(A) The radiolabeled GPx1 SECIS was incubated with SBP2 (0 or 200 nM) and increasing concentrations of eIF4a3 (0 to 200 nM), as indicated, and analyzed by UV-crosslinking. Two different crosslinked products are indicated: eIF4a3-GPx1 SECIS, open triangle; SBP2-GPx1 SECIS, filled triangle. (B) Pre-formed complexes between radiolabeled GPx1 SECIS (1 nM) and varying amounts of eIF4a3 (0 to 200 nM) were challenged with SBP2 (200 nM). Samples were analyzed by UV-crosslinking. (C) Recoding assays with the luc/UGA/GPx1 and luc/UGA/PHGPx reporter RNAs were performed in the absence or presence of 100 ng purified eIF4a3. The RNAs and eIF4a3 were not preincubated or preincubated for 20 minutes prior to in vitro translation, as indicated.
Figure 5
Figure 5. Characterization of the eIF4a3-GPx1 SECIS interaction
(A) Schematic representation of the GPx1 SECIS, with the SECIS core mutations indicated. (B) The mutant RNAs in (A) were tested as competitors (0 to 200 nM) in UV-crosslinking assays containing eIF4a3 and the radiolabeled wild-type GPx1 SECIS probe. The IC50s of the mutant RNAs, which were calculated as described in the legend to Fig. 2, are shown. (C) Schematic representation of the mutations in the internal loop of the GPx1 SECIS. (D) Graphic representation of the results of competition experiments in which cold wild-type and mutant SECIS RNAs were tested for their ability to compete for binding of eIF4a3 to the 32P-labeled GPx1 SECIS element. The IC50s were calculated as described in (B).
Figure 6
Figure 6. Effect of selenium on mRNA and protein expression
(A) Total RNA was extracted from McArdle 7777 cells grown with (+Se) or without (−Se) 30 nM sodium selenite supplementation after 3 days. GPx1, PHGPx, GAPDH, and eIF4a3 mRNA levels were determined by qRT-PCR. The level of mRNA was expressed relative to the amount of mRNA from +Se cells (dashed line). The data are represented as the mean +/− SEM. (B) Cytoplasmic or nuclear extracts were analyzed by Western blotting using different antibodies as indicated. (C) The graph represents quantification of Western blot data from three independent experiments. The results are normalized to GAPDH expression. (D) qRT-PCR crossing points values of GAPDH, GPx1 and PHGPx mRNAs co-immunoprecipitated with anti-eIF4a3 or isotype control antibody. (E) Relative enrichment of GAPDH, GPx1 and PHGPx mRNAs in the eIF4a3 immunoprecipitation compared to the isotype control.
Figure 7
Figure 7. Manipulation of eIF4a3 regulates GPx1 expression in cells
(A) McArdle 7777 cells were treated with different siRNAs for 72 hours as described in Materials and Methods. Cell lysates were analyzed by Western blotting using the indicated antibodies. (B) Quantification of the Western blot data were from 3 independent experiments. The results are normalized to GAPDH and represented as mean +/− SD. (C) McArdle 7777 cells were transiently transfected with empty vector DNA (mock) or a plasmid encoding the human eIF4a3 cDNA. The Western blots (C) and quantification (D) were performed as described in (A) and (B)
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