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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE145465 | GEO | 2022/11/02

REPOSITORIES: GEO

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Project description:Selenoproteins are a small family of proteins containing the trace element selenium in form of the rare amino acid selenocysteine (Sec), which is decoded by the UGA codon. In humans, a number of pathogenic mutations in genes encoding distinct selenoproteins or selenoprotein biosynthesis factors have been identified. Pathogenic mutations in selenocysteine synthase (SEPSECS), which catalyzes the last step in Sec-tRNA[Ser]Sec biosynthesis, were reported in children suffering from progressive cerebello-cerebral atrophy. To understand the underlying mechanisms of SEPSECS mutations, we generated a novel mouse model recapitulating the respective human pathogenic Y334C mutation in the murine Sepsecs gene (SepsecsY334C). Unlike in patients, homozygous mutant pups died perinatally with signs of cardio-respiratory failure. Perinatal death is reminiscent of the Sedaghatian spondylometaphyseal dysplasia disorder in humans, which is caused by inactivating mutations of the gene encoding the selenoprotein and key ferroptosis regulator glutathione peroxidase 4 (GPX4). Protein expression levels of distinct selenoproteins in SepsecsY334C/Y334C mice were found to be generally reduced in brain and isolated cortical neurons, while transcriptomics analysis uncovered an upregulation of NRF2-regulated genes. Crossbreeding of SepsecsY334C/Y334C mice with mice harboring a targeted mutation of the catalytically active site Sec to Cys in GPX4 surprisingly rescued perinatal death of SepsecsY334C/Y334C mice, showing that the cardio-respiratory defects of Sepsecs-mutant mice were caused by the lack of GPX4. Like in SepsecsY334C/Y334C mice, selenoprotein expression levels remained low and NRF2-regulated genes remained highly expressed in these compound mutant mice, indicating that selenium-independent GPX4, along with a sustained antioxidant response are sufficient to compensate for dysfunctional Sec-tRNA[Ser]Sec biosynthesis. Our findings imply that children with mutations in SEPSECS or GPX4 may benefit from treatments partially compensating for impaired GPX4 activity.

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

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