Elongator—a tRNA modifying complex that promotes efficient translational decoding

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Abstract

Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm5) or 5-methoxycarbonylmethyl (mcm5) side-chain and sometimes also a 2-thio or 2′-O-methyl group. The first step in the formation of the ncm5 and mcm5 side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

Section snippets

Uridines at the wobble position in cytoplasmic S. cerevisiae tRNAs

In S. cerevisiae, 42 different tRNA species are responsible for the decoding of the 61 sense codons in cytosolic mRNAs (Fig. 1) [7], [8]. Of these tRNAs, 13 are transcribed with a U at the wobble position. The wobble uridine remains unmodified in tRNAUAGLeu [9] and is isomerized to pseudouridine (Ψ) in tRNAΨAΨIle by the pseudouridine synthase Pus1 (Fig. 1, Fig. 2) [10], [11]. The remaining tRNA species contain an xm5 side-chain on the wobble uridine, where the xm5 group is either a

The Elongator complex

Although the Elongator complex was originally identified as a factor promoting elongation of RNA polymerase II transcription [36], [37], [38], [39], [40], more recent studies have shown that its main, and probably only, cellular function is to promote the formation of ncm5 and mcm5 side-chains on wobble uridines [20], [28], [41]. The six Elp proteins form two distinct sub-complexes composed of Elp1-Elp3 and Elp4-Elp6, respectively [36], [37], [38], [39]. Structural studies of the Elongator

Factors influencing the activity of Elongator

Several different factors have been suggested to influence the activity of Elongator and consequently the formation of the mcm5 and ncm5 side-chains on wobble uridines. These factors include the Kti11, Kti12, Kti13, Hrr25, Sit4, Sap185, Sap190, Cbr1, and Mcr1 proteins. Kti11, also known as Dph3, is a metal-binding protein required for both the synthesis of ncm5/mcm5 side chains and the conversion of a histidine to diphtamide in eukaryotic translation elongation factor 2 (eEF2) [20], [53], [54],

Elongator-dependent nucleoside modifications promote decoding of A- and G-ending codons

The original wobble hypothesis postulated that an unmodified U34 should preferentially pair with A and G at the third position of codons [70]. It has since then become apparent that tRNAs with an unmodified U34 can, at least under some circumstances, pair with codons ending with any of the four bases [71], [72]. Although unmodified wobble uridines are frequently found in tRNAs from organelles and Mycoplasma spp. they are rarely found in cytoplasmic tRNAs from eukaryotes [5]. The only

The pleiotropic phenotypes of yeast cells lacking Elongator-dependent tRNA modifications correlate with inefficient decoding of AAA, CAA and GAA codons

The Elongator complex has, in addition to its role in tRNA modification, been implicated in several unrelated cellular processes, including elongation of RNA polymerase II transcription, telomeric gene silencing, DNA repair, and exocytosis [40], [91], [92], [93]. However, all the phenotypes of Elongator mutants, except the tRNA modification defect, are counteracted by increased expression of various combinations of the hypomodified forms of tRNAmcm5s2UUULys, tRNAmcm5s2UUGGln, and tRNAmcm5s2UUC

Elongator's role in tRNA modification is conserved in eukaryotes

In addition to its role in fungal tRNA modification, Elongator has been shown to promote formation of ncm5 and mcm5 side-chains at wobble uridines in worms, mice, plants, and humans [98], [99], [100], [101], [102]. The inactivation of Elongator induces a variety of different phenotypes also in these organisms and the complex has been suggested to have several distinct functions [41], [45]. Even though it cannot be excluded that Elongator may have additional functions, the phenotypes are likely

Concluding remarks

In all organisms examined to date, the inactivation of Elongator leads to the lack of xm5 side-chains on wobble uridines in tRNA. The effects of the wobble xm5U derivatives on translational efficiency and fidelity provide a likely explanation to the wide variety of phenotypes displayed by Elongator-deficient organisms. However, the cause of the individual phenotypes remains poorly characterized and further studies are needed to define the underlying mechanisms.

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Acknowledgements

Research in the authors laboratories was supported by: Carl Tryggers Foundation (CTS13:206 to MJ); Åke Wibergs Foundation (M14-0207 to MJ); Insamlingsstiftelsen Umeå universitet (FS 2.1.6-1888-15 to MJ); Swedish Research Council (621-2016-03949 to AB); and Karin and Harald Silvanders Foundation/Insamlingsstiftelsen Umeå universitet (FS 2.1.6-1870-16 to AB).

References (110)

  • Y. Nakai et al.

    Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems

    J. Biol. Chem.

    (2008)
  • F. Bauer et al.

    Translational control of cell division by Elongator

    Cell Rep.

    (2012)
  • G. Otero et al.

    Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation

    Mol. Cell

    (1999)
  • G.S. Winkler et al.

    RNA polymerase II Elongator holoenzyme is composed of two discrete subcomplexes

    J. Biol. Chem.

    (2001)
  • Y. Li et al.

    A multiprotein complex that interacts with RNA polymerase II Elongator

    J. Biol. Chem.

    (2001)
  • B.O. Wittschieben et al.

    A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme

    Mol. Cell

    (1999)
  • O. Kolaj-Robin et al.

    Structures and activities of the Elongator complex and its cofactors

    Enzyme

    (2017)
  • Y. Chinenov

    A second catalytic domain in the Elp3 histone acetyltransferases: a candidate for histone demethylase activity?

    Trends Biochem. Sci.

    (2002)
  • S. Glatt et al.

    Structural insights into Elongator function

    Curr. Opin. Struct. Biol.

    (2013)
  • S. Liu et al.

    Retroviral insertional mutagenesis identifies a small protein required for synthesis of diphthamide, the target of bacterial ADP-ribosylating toxins

    Mol. Cell

    (2003)
  • S. Glatt et al.

    Structure of the Kti11/Kti13 heterodimer and its double role in modifications of tRNA and eukaryotic elongation factor 2

    Structure

    (2015)
  • F.H. Crick

    Codon—anticodon pairing: the wobble hypothesis

    J. Mol. Biol.

    (1966)
  • V.I. Lim

    Analysis of action of wobble nucleoside modifications on codon-anticodon pairing within the ribosome

    J. Mol. Biol.

    (1994)
  • J. Weissenbach et al.

    Yeast tRNALeu (anticodon U–A–G) translates all six leucine codons in extracts from interferon treated cells

    FEBS Lett.

    (1977)
  • P.F. Agris

    Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis

    Biochimie

    (1991)
  • T.G. Hagervall et al.

    Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position

    J. Mol. Biol.

    (1998)
  • S. Kurata et al.

    Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding

    J. Biol. Chem.

    (2008)
  • D.D. Nedialkova et al.

    Optimization of codon translation rates via tRNA modifications maintains proteome integrity

    Cell

    (2015)
  • F.A. Vendeix et al.

    Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism

    J. Mol. Biol.

    (2012)
  • U. Begley et al.

    Trm9-catalyzed tRNA modifications link translation to the DNA damage response

    Mol. Cell

    (2007)
  • P.B. Rahl et al.

    Elp1p, the yeast homolog of the FD disease syndrome protein, negatively regulates exocytosis independently of transcriptional elongation

    Mol. Cell

    (2005)
  • M.J.O. Johansson et al.

    Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae

  • E.M. Phizicky et al.

    tRNA biology charges to the front

    Genes Dev.

    (2010)
  • G.R. Björk et al.

    Transfer RNA Modification: Presence, Synthesis, and Function, EcoSal Plus, 6

    (2014)
  • B. El Yacoubi et al.

    Biosynthesis and function of posttranscriptional modifications of transfer RNAs

    Annu. Rev. Genet.

    (2012)
  • M.A. Machnicka et al.

    Distribution and frequencies of post-transcriptional modifications in tRNAs

    RNA Biol.

    (2014)
  • J. Hani et al.

    tRNA genes and retroelements in the yeast genome

    Nucleic Acids Res.

    (1998)
  • E. Randerath et al.

    Yeast tRNA Leu UAG. Purification, properties and determination of the nucleotide sequence by radioactive derivative methods

    Eur. J. Biochem.

    (1979)
  • Z. Szweykowska-Kulinska et al.

    Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile)

    EMBO J.

    (1994)
  • G. Simos et al.

    Nuclear pore proteins are involved in the biogenesis of functional tRNA

    EMBO J.

    (1996)
  • N. Yamamoto et al.

    Modified nucleoside, 5-carbamoylmethyluridine, located in the first position of the anticodon of yeast valine tRNA

    J. Biochem.

    (1985)
  • M.J.O. Johansson et al.

    Eukaryotic wobble uridine modifications promote a functionally redundant decoding system

    Mol. Cell. Biol.

    (2008)
  • J. Lu et al.

    The Kluyveromyces lactis gamma-toxin targets tRNA anticodons

    RNA

    (2005)
  • B. Huang et al.

    An early step in wobble uridine tRNA modification requires the Elongator complex

    RNA

    (2005)
  • H.R. Kalhor et al.

    Novel methyltransferase for modified uridine residues at the wobble position of tRNA

    Mol. Cell. Biol.

    (2003)
  • C. Chen et al.

    Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U

    PLoS One

    (2011)
  • L. Pintard et al.

    Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop

    EMBO J.

    (2002)
  • M.P. Guy et al.

    Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop

    RNA

    (2012)
  • B. Huang et al.

    A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae

    RNA

    (2008)
  • G.R. Björk et al.

    A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast

    RNA

    (2007)
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    This article is part of a special issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

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