Cellular and Molecular Life Sciences

, Volume 75, Issue 9, pp 1613–1622 | Cite as

Structural insights into the function of Elongator

Review

Abstract

Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-l-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity. How at the molecular level, Elongator performs its multiple functions and how the different subunits regulate Elongator’s activities remains poorly understood. Here, we provide an overview of the proposed functions of Elongator and describe how recent structural studies provide new insights into the mechanism of action of this multifunctional complex.

Keywords

Elongator Transcription tRNA modification X-ray crystallography Electron microscopy Familial dysautonomia 

Abbreviations

ATP

Adenosine triphosphate

CoA

Coenzyme A

cm5U

5-carboxymethyluridine

cryo-EM

Cryo electron microscopy

Elp

Elongator protein

EM

Electron microscopy

FD

Familial dysautonomia

GEF

Guanine-nucleotide exchange factor

GNAT

Gcn5-related N-terminal acetyltransferase

HAT

Histone acetyltransferase

IKAP

IκB kinase associated protein

IKBKAP

Inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein

IKI3

Insensitive to killer toxin-3

IκB

Inhibitor of kappa-B

mcm5U

5-Methoxycarbonylmethyluridine

mcm5s2U

5-methoxycarbonylmethyl-2-thiouridine

ncm5U

5-carbamoylmethyluridine

RNAPII

RNA polymerase II

SAM

S-adenosyl-l-methionine

TPR

Tetratricopeptide repeat

WD40

Typtophan-aspartic acid-40

Notes

Acknowledgements

This work was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant (418157-2012), a Canadian Institutes of Health Research (CIHR) Foundation Grant (FDN-143228), a Michael Smith Foundation for Health Research Career Investigator Award, a CIHR New Investigator Award to CY, and an NSERC PGS-D fellowship to U.D.

References

  1. 1.
    Otero G et al (1999) Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell 3:109–118CrossRefPubMedGoogle Scholar
  2. 2.
    Krogan NJ, Greenblatt JF (2001) Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol 21:8203–8212CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Winkler GS, Petrakis TG, Ethelberg S, Tokunaga M, Erdjument-Bromage H, Tempst P, Svejstrup JQ (2001) RNA polymerase II elongator holoenzyme is composed of two discrete subcomplexes. J Biol Chem 276:32743–32749CrossRefPubMedGoogle Scholar
  4. 4.
    Li Y, Takagi Y, Jiang Y, Tokunaga M, Erdjument-Bromage H, Tempst P, Kornberg RD (2001) A multiprotein complex that interacts with RNA polymerase II elongator. J Biol Chem 276:29628–29631CrossRefPubMedGoogle Scholar
  5. 5.
    Hawkes NA et al (2002) Purification and characterization of the human elongator complex. J Biol Chem 277:3047–3052CrossRefPubMedGoogle Scholar
  6. 6.
    Wittschieben BO et al (1999) A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol Cell 4:123–128CrossRefPubMedGoogle Scholar
  7. 7.
    Frohloff F, Fichtner L, Jablonowski D, Breunig KD, Schaffrath R (2001) Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin. EMBO J 20:1993–2003CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Butler AR, White JH, Folawiyo Y, Edlin A, Gardiner D, Stark MJ (1994) Two Saccharomyces cerevisiae genes which control sensitivity to G1 arrest induced by Kluyveromyces lactis toxin. Mol Cell Biol 14:6306–6316CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Kawamoto S et al (1990) Isolation and characterization of mutants of Saccharomyces cerevisiae resistant to killer toxin of Kluyveromyces lactis. J Ferment Bioeng 70:222–227CrossRefGoogle Scholar
  10. 10.
    Kishida M, Tokunaga M, Katayose Y, Yajima H, Kawamura-Watabe A, Hishinuma F (1996) Isolation and genetic characterization of pGKL killer-insensitive mutants (iki) from Saccharomyces cerevisiae. Biosci Biotechnol Biochem 60:798–801CrossRefPubMedGoogle Scholar
  11. 11.
    Chinenov Y (2002) A second catalytic domain in the Elp3 histone acetyltransferases: a candidate for histone demethylase activity? Trends Biochem Sci 27:115–117CrossRefPubMedGoogle Scholar
  12. 12.
    Huang B, Johansson MJ, Bystrom AS (2005) An early step in wobble uridine tRNA modification requires the Elongator complex. RNA 11:424–436CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Selvadurai K, Wang P, Seimetz J, Huang RH (2014) Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism. Nat Chem Biol 10:810–812CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Johansson MJO, Xu F, Bystrom AS (2017) Elongator—a tRNA modifying complex that promotes efficient translational decoding. Biochim Biophys Acta.  https://doi.org/10.1016/j.bbagrm.2017.11.006 Google Scholar
  15. 15.
    Dauden MI, Jaciuk M, Muller CW, Glatt S (2017) Structural asymmetry in the eukaryotic Elongator complex. FEBS Lett.  https://doi.org/10.1002/1873-3468.12865 PubMedGoogle Scholar
  16. 16.
    Kolaj-Robin O, Seraphin B (2017) Structures and activities of the Elongator complex and its cofactors. Enzymes 41:117–149CrossRefPubMedGoogle Scholar
  17. 17.
    Winkler GS, Kristjuhan A, Erdjument-Bromage H, Tempst P, Svejstrup JQ (2002) Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo. Proc Natl Acad Sci USA 99:3517–3522CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Wittschieben BO, Fellows J, Du W, Stillman DJ, Svejstrup JQ (2000) Overlapping roles for the histone acetyltransferase activities of SAGA and elongator in vivo. EMBO J 19:3060–3068CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Kim JH, Lane WS, Reinberg D (2002) Human Elongator facilitates RNA polymerase II transcription through chromatin. Proc Natl Acad Sci USA 99:1241–1246CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Gilbert C, Kristjuhan A, Winkler GS, Svejstrup JQ (2004) Elongator interactions with nascent mRNA revealed by RNA immunoprecipitation. Mol Cell 14:457–464CrossRefPubMedGoogle Scholar
  21. 21.
    Krogan NJ et al (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol 22:6979–6992CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Close P et al (2006) Transcription impairment and cell migration defects in elongator-depleted cells: implication for familial dysautonomia. Mol Cell 22:521–531CrossRefPubMedGoogle Scholar
  23. 23.
    Pokholok DK, Hannett NM, Young RA (2002) Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9:799–809CrossRefPubMedGoogle Scholar
  24. 24.
    Fichtner L, Frohloff F, Jablonowski D, Stark MJ, Schaffrath R (2002) Protein interactions within Saccharomyces cerevisiae Elongator, a complex essential for Kluyveromyces lactis zymocicity. Mol Microbiol 45:817–826CrossRefPubMedGoogle Scholar
  25. 25.
    Esberg A, Huang B, Johansson MJ, Bystrom AS (2006) Elevated levels of two tRNA species bypass the requirement for elongator complex in transcription and exocytosis. Mol Cell 24:139–148CrossRefPubMedGoogle Scholar
  26. 26.
    Lu J, Huang B, Esberg A, Johansson MJ, Bystrom AS (2005) The Kluyveromyces lactis gamma-toxin targets tRNA anticodons. RNA 11:1648–1654CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Chen C, Tuck S, Bystrom AS (2009) Defects in tRNA modification associated with neurological and developmental dysfunctions in Caenorhabditis elegans elongator mutants. PLoS Genet 5:e1000561CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Mehlgarten C et al (2010) Elongator function in tRNA wobble uridine modification is conserved between yeast and plants. Mol Microbiol 76:1082–1094CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Lin FJ, Shen L, Jang CW, Falnes PO, Zhang Y (2013) Ikbkap/Elp1 deficiency causes male infertility by disrupting meiotic progression. PLoS Genet 9:e1003516CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Karlsborn T, Tukenmez H, Chen C, Bystrom AS (2014) Familial dysautonomia (FD) patients have reduced levels of the modified wobble nucleoside mcm(5)s(2)U in tRNA. Biochem Biophys Res Commun 454:441–445CrossRefPubMedGoogle Scholar
  31. 31.
    Yoshida M et al (2015) Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci USA 112:2764–2769CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Johansson MJ, Esberg A, Huang B, Bjork GR, Bystrom AS (2008) Eukaryotic wobble uridine modifications promote a functionally redundant decoding system. Mol Cell Biol 28:3301–3312CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Solinger JA et al (2010) The Caenorhabditis elegans Elongator complex regulates neuronal alpha-tubulin acetylation. PLoS Genet 6:e1000820CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Dong C et al (2015) The Elp2 subunit is essential for elongator complex assembly and functional regulation. Structure 23:1078–1086CrossRefPubMedGoogle Scholar
  35. 35.
    Jackson MZ, Gruner KA, Qin C, Tourtellotte WG (2014) A neuron autonomous role for the familial dysautonomia gene ELP1 in sympathetic and sensory target tissue innervation. Development 141:2452–2461CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Ueki Y, Ramirez G, Salcedo E, Stabio ME, Lefcort F (2016) Loss of Ikbkap causes slow, progressive retinal degeneration in a mouse model of familial dysautonomia. eNeuro.  https://doi.org/10.1523/ENEURO.0143-16.2016
  37. 37.
    Okada Y, Yamagata K, Hong K, Wakayama T, Zhang Y (2010) A role for the elongator complex in zygotic paternal genome demethylation. Nature 463:554–558CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Laguesse S et al (2015) A dynamic unfolded protein response contributes to the control of cortical neurogenesis. Dev Cell 35:553–567CrossRefPubMedGoogle Scholar
  39. 39.
    Ohlen SB, Russell ML, Brownstein MJ, Lefcort F (2017) BGP-15 prevents the death of neurons in a mouse model of familial dysautonomia. Proc Natl Acad Sci USA 114:5035–5040CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Nelissen H et al (2003) DRL1, a homolog of the yeast TOT4/KTI12 protein, has a function in meristem activity and organ growth in plants. Plant Cell 15:639–654CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Nelissen H et al (2005) The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth. Proc Natl Acad Sci USA 102:7754–7759CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Falcone A, Nelissen H, Fleury D, Van Lijsebettens M, Bitonti MB (2007) Cytological investigations of the Arabidopsis thaliana elo1 mutant give new insights into leaf lateral growth and Elongator function. Ann Bot 100:261–270CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Zhou X, Hua D, Chen Z, Zhou Z, Gong Z (2009) Elongator mediates ABA responses, oxidative stress resistance and anthocyanin biosynthesis in Arabidopsis. Plant J 60:79–90CrossRefPubMedGoogle Scholar
  44. 44.
    DeFraia CT, Zhang X, Mou Z (2010) Elongator subunit 2 is an accelerator of immune responses in Arabidopsis thaliana. Plant J 64:511–523CrossRefPubMedGoogle Scholar
  45. 45.
    Anderson SL, Coli R, Daly IW, Kichula EA, Rork MJ, Volpi SA, Ekstein J, Rubin BY (2001) Familial dysautonomia is caused by mutations of the IKAP gene. Am J Hum Genet 68:753–758CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Slaugenhaupt SA et al (2001) Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia. Am J Hum Genet 68:598–605CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Cuajungco MP et al (2003) Tissue-specific reduction in splicing efficiency of IKBKAP due to the major mutation associated with familial dysautonomia. Am J Hum Genet 72:749–758CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Hug N, Longman D, Caceres JF (2016) Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 44:1483–1495CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Boone N, Bergon A, Loriod B, Deveze A, Nguyen C, Axelrod FB, Ibrahim EC (2012) Genome-wide analysis of familial dysautonomia and kinetin target genes with patient olfactory ecto-mesenchymal stem cells. Hum Mutat 33:530–540CrossRefPubMedGoogle Scholar
  50. 50.
    Cohen JS, Srivastava S, Farwell KD, Lu HM, Zeng W, Lu H, Chao EC, Fatemi A (2015) ELP2 is a novel gene implicated in neurodevelopmental disabilities. Am J Med Genet A 167:1391–1395CrossRefPubMedGoogle Scholar
  51. 51.
    Simpson CL et al (2009) Variants of the elongator protein 3 (ELP3) gene are associated with motor neuron degeneration. Hum Mol Genet 18:472–481CrossRefPubMedGoogle Scholar
  52. 52.
    Kwee LC et al (2012) A high-density genome-wide association screen of sporadic ALS in US veterans. PLoS One 7:e32768CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Reinthaler EM et al (2014) Analysis of ELP4, SRPX2, and interacting genes in typical and atypical rolandic epilepsy. Epilepsia 55:e89–e93CrossRefPubMedGoogle Scholar
  54. 54.
    Strug LJ et al (2009) Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4). Eur J Hum Genet 17:1171–1181CrossRefPubMedPubMedCentralGoogle Scholar
  55. 55.
    Addis L et al (2015) Microdeletions of ELP4 are associated with language impairment, autism spectrum disorder, and mental retardation. Hum Mutat 36:842–850CrossRefPubMedGoogle Scholar
  56. 56.
    Di Santo R, Bandau S, Stark MJ (2014) A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex. Mol Microbiol 92:1227–1242CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Mehlgarten C, Jablonowski D, Breunig KD, Stark MJ, Schaffrath R (2009) Elongator function depends on antagonistic regulation by casein kinase Hrr25 and protein phosphatase Sit4. Mol Microbiol 73:869–881CrossRefPubMedGoogle Scholar
  58. 58.
    Abdel-Fattah W et al (2015) Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS Genet 11:e1004931CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Xu H et al (2015) Dimerization of elongator protein 1 is essential for Elongator complex assembly. Proc Natl Acad Sci USA 112:10697–10702CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Chaverra M et al (2017) The familial dysautonomia disease gene IKBKAP is required in the developing and adult mouse central nervous system. Dis Model Mech 10:605–618CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Rahl PB, Chen CZ, Collins RN (2005) Elp1p, the yeast homolog of the FD disease syndrome protein, negatively regulates exocytosis independently of transcriptional elongation. Mol Cell 17:841–853CrossRefPubMedGoogle Scholar
  62. 62.
    Fellows J, Erdjument-Bromage H, Tempst P, Svejstrup JQ (2000) The Elp2 subunit of elongator and elongating RNA polymerase II holoenzyme is a WD40 repeat protein. J Biol Chem 275:12896–12899CrossRefPubMedGoogle Scholar
  63. 63.
    Dauden MI et al (2017) Architecture of the yeast Elongator complex. EMBO Rep 18:264–279CrossRefPubMedGoogle Scholar
  64. 64.
    Creppe C et al (2009) Elongator controls the migration and differentiation of cortical neurons through acetylation of alpha-tubulin. Cell 136:551–564CrossRefPubMedGoogle Scholar
  65. 65.
    Paraskevopoulou C, Fairhurst SA, Lowe DJ, Brick P, Onesti S (2006) The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine. Mol Microbiol 59:795–806CrossRefPubMedGoogle Scholar
  66. 66.
    Greenwood C, Selth LA, Dirac-Svejstrup AB, Svejstrup JQ (2009) An iron–sulfur cluster domain in Elp3 important for the structural integrity of elongator. J Biol Chem 284:141–149CrossRefPubMedGoogle Scholar
  67. 67.
    Kolaj-Robin O, McEwen AG, Cavarelli J, Seraphin B (2015) Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRNA modification. FEBS J 282:819–833CrossRefPubMedGoogle Scholar
  68. 68.
    Glatt S et al (2015) Structure of the Kti11/Kti13 heterodimer and its double role in modifications of tRNA and eukaryotic elongation factor 2. Structure 23:149–160CrossRefPubMedGoogle Scholar
  69. 69.
    Glatt S et al (2016) Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Nat Struct Mol Biol 23:794–802CrossRefPubMedPubMedCentralGoogle Scholar
  70. 70.
    Glatt S, Letoquart J, Faux C, Taylor NM, Seraphin B, Muller CW (2012) The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase. Nat Struct Mol Biol 19:314–320CrossRefPubMedGoogle Scholar
  71. 71.
    Lin Z, Zhao W, Diao W, Xie X, Wang Z, Zhang J, Shen Y, Long J (2012) Crystal structure of elongator subcomplex Elp4-6. J Biol Chem 287:21501–21508CrossRefPubMedPubMedCentralGoogle Scholar
  72. 72.
    Setiaputra DT et al (2017) Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement. EMBO Rep 18:280–291CrossRefPubMedGoogle Scholar
  73. 73.
    Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O’Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–741CrossRefPubMedGoogle Scholar
  74. 74.
    Kuhlbrandt W (2014) Biochemistry. The resolution revolution. Science 343:1443–1444CrossRefPubMedGoogle Scholar
  75. 75.
    Smith MT, Rubinstein JL (2014) Structural biology. Beyond blob-ology. Science 345:617–619CrossRefPubMedGoogle Scholar
  76. 76.
    Dalvai M, Loehr J, Jacquet K, Huard CC, Roques C, Herst P, Cote J, Doyon Y (2015) A scalable genome-editing-based approach for mapping multiprotein complexes in human cells. Cell Rep 13:621–633CrossRefPubMedGoogle Scholar
  77. 77.
    Sun J et al (2005) Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module. Biochemistry 44:8801–8809CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular BiologyThe University of British ColumbiaVancouverCanada

Personalised recommendations