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

Abstract 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.

[1]  M. T. Howard,et al.  Avoidance of reporter assay distortions from fused dual reporters , 2017, RNA.

[2]  C. Anderson,et al.  The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay , 2016, Nucleic acids research.

[3]  H. Grubmüller,et al.  The pathway to GTPase activation of elongation factor SelB on the ribosome , 2016, Nature.

[4]  R. Guigó,et al.  Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements , 2016, Open Biology.

[5]  R. Guigó,et al.  Selenoprotein Gene Nomenclature* , 2016, The Journal of Biological Chemistry.

[6]  R. Burk,et al.  Regulation of Selenium Metabolism and Transport. , 2015, Annual review of nutrition.

[7]  K. Khoo,et al.  CRL2 aids elimination of truncated selenoproteins produced by failed UGA/Sec decoding , 2015, Science.

[8]  Ravi V. Shah,et al.  Regulation of Selenocysteine Incorporation into the Selenium Transport Protein, Selenoprotein P* , 2014, The Journal of Biological Chemistry.

[9]  F. Martin,et al.  Hypermethylated-capped selenoprotein mRNAs in mammals , 2014, Nucleic acids research.

[10]  V. Gladyshev,et al.  Selenoproteins: molecular pathways and physiological roles. , 2014, Physiological reviews.

[11]  Kristie L. Rose,et al.  Sepp1(UF) forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1. , 2014, Free radical biology & medicine.

[12]  D. Driscoll,et al.  Alternative Transcripts and 3′UTR Elements Govern the Incorporation of Selenocysteine into Selenoprotein S , 2013, PloS one.

[13]  Serge Gueroussov,et al.  RanBP2/Nup358 Potentiates the Translation of a Subset of mRNAs Encoding Secretory Proteins , 2013, PLoS biology.

[14]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[15]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[16]  J. Donovan,et al.  The efficiency of selenocysteine incorporation is regulated by translation initiation factors. , 2010, Journal of molecular biology.

[17]  S. M. Fixsen,et al.  Processive selenocysteine incorporation during synthesis of eukaryotic selenoproteins. , 2010, Journal of molecular biology.

[18]  Michael E. Budiman,et al.  Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression , 2010, Nucleic acids research.

[19]  Michael E. Budiman,et al.  Eukaryotic initiation factor 4a3 is a selenium-regulated RNA-binding protein that selectively inhibits selenocysteine incorporation. , 2009, Molecules and Cells.

[20]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[21]  Mark W. Moyle,et al.  A mutation in the SEPN1 selenocysteine redefinition element (SRE) reduces selenocysteine incorporation and leads to SEPN1‐related myopathy , 2009, Human mutation.

[22]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[23]  V. Gladyshev,et al.  Reduced reliance on the trace element selenium during evolution of mammals , 2008, Genome Biology.

[24]  T. Rapoport,et al.  The Signal Sequence Coding Region Promotes Nuclear Export of mRNA , 2007, PLoS biology.

[25]  Mark W. Moyle,et al.  A recoding element that stimulates decoding of UGA codons by Sec tRNA[Ser]Sec. , 2007, RNA.

[26]  J. Harney,et al.  Efficient Incorporation of Multiple Selenocysteines Involves an Inefficient Decoding Step Serving as a Potential Translational Checkpoint and RibosomeBottleneck , 2006, Molecular and Cellular Biology.

[27]  M. T. Howard,et al.  Recoding elements located adjacent to a subset of eukaryal selenocysteine‐specifying UGA codons , 2005, The EMBO journal.

[28]  L. Chavatte,et al.  Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes , 2005, Nature Structural &Molecular Biology.

[29]  Peter F Stadler,et al.  Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.

[30]  J. Harney,et al.  Coupled tRNA(Sec)-dependent assembly of the selenocysteine decoding apparatus. , 2003, Molecular cell.

[31]  R. Caprioli,et al.  Mass Spectrometric Characterization of Full-length Rat Selenoprotein P and Three Isoforms Shortened at the C Terminus , 2002, The Journal of Biological Chemistry.

[32]  Vincent Stepanik,et al.  Insight into Mammalian Selenocysteine Insertion: Domain Structure and Ribosome Binding Properties of Sec Insertion Sequence Binding Protein 2 , 2001, Molecular and Cellular Biology.

[33]  G. Kryukov,et al.  Selenium metabolism in zebrafish: multiplicity of selenoprotein genes and expression of a protein containing 17 selenocysteine residues , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[34]  P. Carbon,et al.  Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation , 2000, The EMBO journal.

[35]  J. Harney,et al.  Decoding apparatus for eukaryotic selenocysteine insertion , 2000, EMBO reports.

[36]  B. Carlson,et al.  A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs , 2000, The EMBO journal.

[37]  R. Burk,et al.  Isoforms of Selenoprotein P in Rat Plasma , 1996, The Journal of Biological Chemistry.

[38]  M. Berry,et al.  Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. , 1993, The EMBO journal.

[39]  P. Newburger,et al.  Sequences in the 3'-untranslated region of the human cellular glutathione peroxidase gene are necessary and sufficient for selenocysteine incorporation at the UGA codon. , 1993, The Journal of biological chemistry.

[40]  R. Lloyd,et al.  Conserved nucleotide sequences in the open reading frame and 3' untranslated region of selenoprotein P mRNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[41]  M. Berry,et al.  Recognition of UGA as a selenocysteine codon in Type I deiodinase requires sequences in the 3′ untranslated region , 1991, Nature.

[42]  A. Böck,et al.  Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Stefan Aachen,et al.  Recoding Expansion Of Decoding Rules Enriches Gene Expression , 2016 .

[44]  Pacific Symposium on Biocomputing 15:69-79(2010) RNAZ 2.0: IMPROVED NONCODING RNA DETECTION , 2022 .