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New Directions for Understanding the Codon Redefinition Required for Selenocysteine Incorporation

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Abstract

The fact that selenocysteine (Sec) is delivered to the elongating ribosome by a tRNA that recognizes a UGA stop codon makes it unique and a thorn in the side of what was originally thought to be a universal genetic code. The mechanism by which this redefinition occurs has been slowly coming to light over the past 30 years, but key questions remain. This review seeks to highlight the prominent mechanistic questions that will guide the direction of work in the near future. These questions arise from two major aspects of Sec incorporation: (1) novel functions for the Sec insertion sequence (SECIS) that resides in all selenoprotein mRNAs and (2) the myriad of RNA-binding proteins, both known and yet to be discovered, that act in concert to modify the translation elongation process to allow Sec incorporation.

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References

  1. Gupta N, DeMong LW, Banda S, Copeland PR (2013) Reconstitution of selenocysteine incorporation reveals intrinsic regulation by SECIS elements. J Mol Biol 425(14):2415–2422. https://doi.org/10.1016/j.jmb.2013.04.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Latreche L, Jean-Jean O, Driscoll DM, Chavatte L (2009) Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine. Nucleic Acids Res 37(17):5868–5880. https://doi.org/10.1093/nar/gkp635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Klein DJ, Schmeing TM, Moore PB, Steitz TA (2001) The kink-turn: a new RNA secondary structure motif. EMBO J 20(15):4214–4221. https://doi.org/10.1093/emboj/20.15.4214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Donovan J, Copeland PR (2012) Selenocysteine insertion sequence binding protein 2L is implicated as a novel post-transcriptional regulator of selenoprotein expression. PLoS One 7(4):e35581. https://doi.org/10.1371/journal.pone.0035581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Shetty SP, Sturts R, Vetick M, Copeland PR (2018) Processive incorporation of multiple selenocysteine residues is driven by a novel feature of the selenocysteine insertion sequence. J Biol Chem 293(50):19377–19386. https://doi.org/10.1074/jbc.RA118.005211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Mariotti M, Shetty S, Baird L, Wu S, Loughran G, Copeland PR, Atkins JF, Howard MT (2017) Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P. Nucleic Acids Res 45(22):13004–13015. https://doi.org/10.1093/nar/gkx982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Berry MJ, Kieffer JD, Larsen PR (1991) Evidence that cysteine, not selenocysteine, is in the catalytic site of type II iodothyronine deiodinase. Endocrinology 129(1):550–552. https://doi.org/10.1210/endo-129-1-550

    Article  CAS  PubMed  Google Scholar 

  8. Berry MJ, Larsen PR (1993) Molecular cloning of the selenocysteine-containing enzyme type I iodothyronine deiodinase. Am J Clin Nutr 57(2 Suppl):249S–255S. https://doi.org/10.1093/ajcn/57.2.249S

    Article  CAS  PubMed  Google Scholar 

  9. Fletcher JE, Copeland PR, Driscoll DM, Krol A (2001) The selenocysteine incorporation machinery: interactions between the SECIS RNA and the SECIS-binding protein SBP2. RNA 7(10):1442–1453

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Gonzalez-Flores JN, Gupta N, DeMong LW, Copeland PR (2012) The selenocysteine-specific elongation factor contains a novel and multi-functional domain. J Biol Chem 287(46):38936–38945. https://doi.org/10.1074/jbc.M112.415463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Howard MT, Moyle MW, Aggarwal G, Carlson BA, Anderson CB (2007) A recoding element that stimulates decoding of UGA codons by Sec tRNA [Ser]Sec. RNA 13(6):912–920. https://doi.org/10.1261/rna.473907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Maiti B, Arbogast S, Allamand V, Moyle MW, Anderson CB, Richard P, Guicheney P, Ferreiro A, Flanigan KM, Howard MT (2009) A mutation in the SEPN1 selenocysteine redefinition element (SRE) reduces selenocysteine incorporation and leads to SEPN1-related myopathy. Hum Mutat 30(3):411–416. https://doi.org/10.1002/humu.20879

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schroder GF, Grubmuller H, Ficner R, Rodnina MV, Stark H (2016) The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 540(7631):80–85. https://doi.org/10.1038/nature20560

    Article  CAS  PubMed  Google Scholar 

  14. Zinoni F, Heider J, Bock A (1990) Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci U S A 87(12):4660–4664

    Article  CAS  Google Scholar 

  15. Heider J, Baron C, Bock A (1992) Coding from a distance: dissection of the mRNA determinants required for the incorporation of selenocysteine into protein. EMBO J 11(10):3759–3766

    Article  CAS  Google Scholar 

  16. Baron C, Heider J, Bock A (1993) Interaction of translation factor SELB with the formate dehydrogenase H selenopolypeptide mRNA. Proc Natl Acad Sci U S A 90(9):4181–4185

    Article  CAS  Google Scholar 

  17. Mariotti M, Shetty S, Baird L, Wu S, Loughran G, Copeland PR, Atkins JF, Howard MT (2017) Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P. Nucleic Acids Res 45:13004–13015. https://doi.org/10.1093/nar/gkx982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Stoytcheva Z, Tujebajeva RM, Harney JW, Berry MJ (2006) Efficient incorporation of multiple selenocysteines involves an inefficient decoding step serving as a potential translational checkpoint and ribosome bottleneck. Mol Cell Biol 26(24):9177–9184. https://doi.org/10.1128/MCB.00856-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Shetty SP, Shah R, Copeland PR (2014) Regulation of selenocysteine incorporation into the selenium transport protein, selenoprotein P. J Biol Chem 289(36):25317–25326. https://doi.org/10.1074/jbc.M114.590430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wu S, Mariotti M, Santesmasses D, Hill KE, Baclaocos J, Aparicio-Prat E, Li S, Mackrill J, Wu Y, Howard MT, Capecchi M, Guigo R, Burk RF, Atkins JF (2016) 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. Open Biol 6(11). https://doi.org/10.1098/rsob.160241

    Article  Google Scholar 

  21. Fixsen SM, Howard MT (2010) Processive selenocysteine incorporation during synthesis of eukaryotic selenoproteins. J Mol Biol 399(3):385–396. https://doi.org/10.1016/j.jmb.2010.04.033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Gerstberger S, Hafner M, Tuschl T (2014) A census of human RNA-binding proteins. Nat Rev Genet 15(12):829–845. https://doi.org/10.1038/nrg3813

    Article  CAS  PubMed  Google Scholar 

  23. Glisovic T, Bachorik JL, Yong J, Dreyfuss G (2008) RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 582(14):1977–1986. https://doi.org/10.1016/j.febslet.2008.03.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Budiman ME, Bubenik JL, Miniard AC, Middleton LM, Gerber CA, Cash A, Driscoll DM (2009) Eukaryotic initiation factor 4a3 is a selenium-regulated RNA-binding protein that selectively inhibits selenocysteine incorporation. Mol Cell 35(4):479–489. https://doi.org/10.1016/j.molcel.2009.06.026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Chavatte L, Brown BA, Driscoll DM (2005) Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes. Nat Struct Mol Biol 12(5):408–416. https://doi.org/10.1038/nsmb922

    Article  CAS  PubMed  Google Scholar 

  26. Copeland PR, Driscoll DM (1999) Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis. J Biol Chem 274(36):25447–25454

    Article  CAS  Google Scholar 

  27. Miniard AC, Middleton LM, Budiman ME, Gerber CA, Driscoll DM (2010) Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression. Nucleic Acids Res. https://doi.org/10.1093/nar/gkq247

    Article  CAS  Google Scholar 

  28. de Jesus LA, Hoffmann PR, Michaud T, Forry EP, Small-Howard A, Stillwell RJ, Morozova N, Harney JW, Berry MJ (2006) Nuclear assembly of UGA decoding complexes on selenoprotein mRNAs: a mechanism for eluding nonsense-mediated decay? Mol Cell Biol 26(5):1795–1805. https://doi.org/10.1128/MCB.26.5.1795-1805.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Small-Howard A, Morozova N, Stoytcheva Z, Forry EP, Mansell JB, Harney JW, Carlson BA, Xu XM, Hatfield DL, Berry MJ (2006) Supramolecular complexes mediate selenocysteine incorporation in vivo. Mol Cell Biol 26(6):2337–2346. https://doi.org/10.1128/MCB.26.6.2337-2346.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Copeland PR, Fletcher JE, Carlson BA, Hatfield DL, Driscoll DM (2000) A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs. EMBO J 19(2):306–314. https://doi.org/10.1093/emboj/19.2.306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Copeland PR, Stepanik VA, Driscoll DM (2001) Insight into mammalian selenocysteine insertion: domain structure and ribosome binding properties of Sec insertion sequence binding protein 2. Mol Cell Biol 21(5):1491–1498. https://doi.org/10.1128/MCB.21.5.1491-1498.2001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Donovan J, Caban K, Ranaweera R, Gonzalez-Flores JN, Copeland PR (2008) A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment. J Biol Chem 283(50):35129–35139. https://doi.org/10.1074/jbc.M806008200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kossinova O, Malygin A, Krol A, Karpova G (2014) The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA. RNA 20(7):1046–1056. https://doi.org/10.1261/rna.044917.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Caban K, Copeland PR (2012) Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes. J Biol Chem 287(13):10664–10673. https://doi.org/10.1074/jbc.M111.320929

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Fradejas-Villar N, Seeher S, Anderson CB, Doengi M, Carlson BA, Hatfield DL, Schweizer U, Howard MT (2016) The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay. Nucleic Acids Res 45:4094–4107. https://doi.org/10.1093/nar/gkw1255

    Article  CAS  PubMed Central  Google Scholar 

  36. Dubey A, Copeland PR (2016) The selenocysteine-specific elongation factor contains unique sequences that are required for both nuclear export and selenocysteine incorporation. PLoS One 11(11):e0165642. https://doi.org/10.1371/journal.pone.0165642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Mariotti M, Salinas G, Gabaldon T, Gladyshev VN (2019) Utilization of selenocysteine in early-branching fungal phyla. Nat Microbiol 4:759–765. https://doi.org/10.1038/s41564-018-0354-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Chan CC, Dostie J, Diem MD, Feng W, Mann M, Rappsilber J, Dreyfuss G (2004) eIF4A3 is a novel component of the exon junction complex. RNA 10(2):200–209

    Article  CAS  Google Scholar 

  39. Ferraiuolo MA, Lee CS, Ler LW, Hsu JL, Costa-Mattioli M, Luo MJ, Reed R, Sonenberg N (2004) A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay. Proc Natl Acad Sci U S A 101(12):4118–4123. https://doi.org/10.1073/pnas.0400933101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Palacios IM, Gatfield D, St Johnston D, Izaurralde E (2004) An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427(6976):753–757. https://doi.org/10.1038/nature02351

    Article  CAS  PubMed  Google Scholar 

  41. Shibuya T, Tange TO, Sonenberg N, Moore MJ (2004) eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat Struct Mol Biol 11(4):346–351. https://doi.org/10.1038/nsmb750

    Article  CAS  PubMed  Google Scholar 

  42. Halic M, Becker T, Frank J, Spahn CM, Beckmann R (2005) Localization and dynamic behavior of ribosomal protein L30e. Nat Struct Mol Biol 12(5):467–468. https://doi.org/10.1038/nsmb933

    Article  CAS  PubMed  Google Scholar 

  43. Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N (2011) Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science 334(6058):941–948. https://doi.org/10.1126/science.1211204

    Article  CAS  PubMed  Google Scholar 

  44. Dabeva MD, Warner JR (1993) Ribosomal protein L32 of Saccharomyces cerevisiae regulates both splicing and translation of its own transcript. J Biol Chem 268(26):19669–19674

    CAS  PubMed  Google Scholar 

  45. Macias S, Bragulat M, Tardiff DF, Vilardell J (2008) L30 binds the nascent RPL30 transcript to repress U2 snRNP recruitment. Mol Cell 30(6):732–742. https://doi.org/10.1016/j.molcel.2008.05.002

    Article  CAS  PubMed  Google Scholar 

  46. Bifano AL, Atassi T, Ferrara T, Driscoll DM (2013) Identification of nucleotides and amino acids that mediate the interaction between ribosomal protein L30 and the SECIS element. BMC Mol Biol 14:12. https://doi.org/10.1186/1471-2199-14-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Jia W, Yao Z, Zhao J, Guan Q, Gao L (2017) New perspectives of physiological and pathological functions of nucleolin (NCL). Life Sci 186:1–10. https://doi.org/10.1016/j.lfs.2017.07.025

    Article  CAS  PubMed  Google Scholar 

  48. Sonenberg N (2008) eIF4E, the mRNA cap-binding protein: from basic discovery to translational research. Biochem Cell Biol 86(2):178–183. https://doi.org/10.1139/O08-034

    Article  CAS  PubMed  Google Scholar 

  49. Wurth L, Gribling-Burrer AS, Verheggen C, Leichter M, Takeuchi A, Baudrey S, Martin F, Krol A, Bertrand E, Allmang C (2014) Hypermethylated-capped selenoprotein mRNAs in mammals. Nucleic Acids Res 42(13):8663–8677. https://doi.org/10.1093/nar/gku580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Gribling-Burrer AS, Leichter M, Wurth L, Huttin A, Schlotter F, Troffer-Charlier N, Cura V, Barkats M, Cavarelli J, Massenet S, Allmang C (2017) SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation. Nucleic Acids Res 45(9):5399–5413. https://doi.org/10.1093/nar/gkx031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Chaytow H, Huang YT, Gillingwater TH, Faller KME (2018) The role of survival motor neuron protein (SMN) in protein homeostasis. Cell Mol Life Sci 75(21):3877–3894. https://doi.org/10.1007/s00018-018-2849-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Li DK, Tisdale S, Lotti F, Pellizzoni L (2014) SMN control of RNP assembly: from post-transcriptional gene regulation to motor neuron disease. Semin Cell Dev Biol 32:22–29. https://doi.org/10.1016/j.semcdb.2014.04.026

    Article  CAS  PubMed  Google Scholar 

  53. Donlin-Asp PG, Fallini C, Campos J, Chou CC, Merritt ME, Phan HC, Bassell GJ, Rossoll W (2017) The survival of motor neuron protein acts as a molecular chaperone for mRNP assembly. Cell Rep 18(7):1660–1673. https://doi.org/10.1016/j.celrep.2017.01.059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Howard MT, Aggarwal G, Anderson CB, Khatri S, Flanigan KM, Atkins JF (2005) Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J 24(8):1596–1607. https://doi.org/10.1038/sj.emboj.7600642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Turanov AA, Lobanov AV, Fomenko DE, Morrison HG, Sogin ML, Klobutcher LA, Hatfield DL, Gladyshev VN (2009) Genetic code supports targeted insertion of two amino acids by one codon. Science 323(5911):259–261. https://doi.org/10.1126/science.1164748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Turanov AA, Lobanov AV, Hatfield DL, Gladyshev VN (2013) UGA codon position-dependent incorporation of selenocysteine into mammalian selenoproteins. Nucleic Acids Res 41(14):6952–6959. https://doi.org/10.1093/nar/gkt409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Labunskyy VM, Hatfield DL, Gladyshev VN (2014) Selenoproteins: molecular pathways and physiological roles. Physiol Rev 94(3):739–777. https://doi.org/10.1152/physrev.00039.2013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by National Institutes of Health grants GM077073 (PRC) and GM114291 (MTH).

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Howard, M.T., Copeland, P.R. New Directions for Understanding the Codon Redefinition Required for Selenocysteine Incorporation. Biol Trace Elem Res 192, 18–25 (2019). https://doi.org/10.1007/s12011-019-01827-y

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