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Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein p

ABSTRACT: Mice carrying genomic deletions of SECIS1 or SECIS2 in the Selenop gene were euthanized and liver tissue was harvested and processed for RNA-Seq and ribosome profiling. From these studies, we determined the affect of SECIS1 and SECIS2 on UGA redifinition across the Selenop gene.

ORGANISM(S): Mus musculus

PROVIDER: GSE102890 | GEO | 2017/08/22

SECONDARY ACCESSION(S): PRJNA399166

REPOSITORIES: GEO

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Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P.

Project description:Gene-specific expansion of the genetic code allows for UGA codons to specify the amino acid selenocysteine (Sec). A striking example of UGA redefinition occurs during translation of the mRNA coding for the selenium transport protein, selenoprotein P (SELENOP), which in vertebrates may contain up to 22 in-frame UGA codons. Sec incorporation at the first and downstream UGA codons occurs with variable efficiencies to control synthesis of full-length and truncated SELENOP isoforms. To address how the Selenop mRNA can direct dynamic codon redefinition in different regions of the same mRNA, we undertook a comprehensive search for phylogenetically conserved RNA structures and examined the function of these structures using cell-based assays, in vitro translation systems, and in vivo ribosome profiling of liver tissue from mice carrying genomic deletions of 3' UTR selenocysteine-insertion-sequences (SECIS1 and SECIS2). The data support a novel RNA structure near the start codon that impacts translation initiation, structures located adjacent to UGA codons, additional coding sequence regions necessary for efficient production of full-length SELENOP, and distinct roles for SECIS1 and SECIS2 at UGA codons. Our results uncover a remarkable diversity of RNA elements conducting multiple occurrences of UGA redefinition to control the synthesis of full-length and truncated SELENOP isoforms.

| S-EPMC5727441 | biostudies-literature

High resolution ribosome profiling reveals gene-specific details of UGA recoding in selenoprotein biosynthesis

Project description:SECIS binding protein 2 (SECISBP2) increases the efficiency of recoding of UGA codons as selenocysteine (Sec) during translation of mRNAs containing a selenocysteine insertion sequence (SECIS) in the 3’-untranslated region. Using ribosomal profiling, we have previously studied selenoprotein translation in hepatocyte-specific Secisbp2-deficient mouse liver and neuron-specific Secisbp2-mutant mouse brain. The use of organs carries the limitation of cellular heterogeneity with cells still expressing wild-type SECISBP2 that might potentially confound analyses and conclusions. To address this concern, we studied a haploid human HAP1 cell line carrying a non-functional SECISBP2 protein. These cells are still capable of metabolically incorporating 75Se into selenoproteins. We performed ribosomal profiling, and show that the efficiency of UGA recoding is gene-specific in SECISBP2- deficient cells. Analysis of ribosomes with UGA either at the A-site or the P-site revealed in a transcript-specific manner that SECISBP2 helps to recruit tRNASec and stabilizes mRNA. We propose a new measure to assess UGA/Sec read-through at codon resolution in all selenoproteins, i.e. the proportion of ribosomes carrying UGA in the P-site, pUGA. An additional, new observation is frame- shifting occurring after the UGA/Sec codon in GPX1, SELENOF, and SELENOW in HAP1 cells, a finding corroborated by reanalysis of neuron-specific Secisbp2-mutant brains.

2022-11-02 | GSE145465 | GEO

Global analysis of selenoprotein expression reveals differential roles for Secisbp2 in UGA redefinition and mRNA stabilization

Project description:We describe the effects of knocking out the Secisbp2 and Trsp genes on selenoprotein expression and translation in mouse liver

2016-10-30 | GSE84112 | GEO

Translational redefinition of UGA codons is regulated by selenium availability.

Project description:Incorporation of selenium into ~25 mammalian selenoproteins occurs by translational recoding whereby in-frame UGA codons are redefined to encode the selenium containing amino acid, selenocysteine (Sec). Here we applied ribosome profiling to examine the effect of dietary selenium levels on the translational mechanisms controlling selenoprotein synthesis in mouse liver. Dietary selenium levels were shown to control gene-specific selenoprotein expression primarily at the translation level by differential regulation of UGA redefinition and Sec incorporation efficiency, although effects on translation initiation and mRNA abundance were also observed. Direct evidence is presented that increasing dietary selenium causes a vast increase in ribosome density downstream of UGA-Sec codons for a subset of selenoprotein mRNAs and that the selenium-dependent effects on Sec incorporation efficiency are mediated in part by the degree of Sec-tRNA([Ser]Sec) Um34 methylation. Furthermore, we find evidence for translation in the 5'-UTRs for a subset of selenoproteins and for ribosome pausing near the UGA-Sec codon in those mRNAs encoding the selenoproteins most affected by selenium availability. These data illustrate how dietary levels of the trace element selenium can alter the readout of the genetic code to affect the expression of an entire class of proteins.

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Identification of the Selenoprotein S Positive UGA Recoding (SPUR) element and its position-dependent activity.

Project description:Selenoproteins are a unique class of proteins that contain the 21st amino acid, selenocysteine (Sec). Addition of Sec into a protein is achieved by recoding of the UGA stop codon. All 25 mammalian selenoprotein mRNAs possess a 3' UTR stem-loop structure, the Selenocysteine Insertion Sequence (SECIS), which is required for Sec incorporation. It is widely believed that the SECIS is the major RNA element that controls Sec insertion, however recent findings in our lab suggest otherwise for Selenoprotein S (SelS). Here we report that the first 91 nucleotides of the SelS 3' UTR contain a proximal stem loop (PSL) and a conserved sequence we have named the SelS Positive UGA Recoding (SPUR) element. We developed a SelS-V5/UGA surrogate assay for UGA recoding, which was validated by mass spectrometry to be an accurate measure of Sec incorporation in cells. Using this assay, we show that point mutations in the SPUR element greatly reduce recoding in the reporter; thus, the SPUR is required for readthrough of the UGA-Sec codon. In contrast, deletion of the PSL increased Sec incorporation. This effect was reversed when the PSL was replaced with other stem-loops or an unstructured sequence, suggesting that the PSL does not play an active role in Sec insertion. Additional studies revealed that the position of the SPUR relative to the UGA-Sec codon is important for optimal UGA recoding. Our identification of the SPUR element in the SelS 3' UTR reveals a more complex regulation of Sec incorporation than previously realized.

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