Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Elongator—a tRNA modifying complex that promotes efficient translational decoding☆
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 [9] and is isomerized to pseudouridine (Ψ) in 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 , , and
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).
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Same but different — Molecular comparison of human KTI12 and PSTK
2021, Biochimica et Biophysica Acta - Molecular Cell ResearchCitation Excerpt :Subsequently, Kti12 was shown to act as a direct, but temporarily associated regulatory factor of the eukaryotic Elongator complex [3,4]. Elongator is a conserved, multi-subunit complex [5,6] responsible for the 5-carboxymethyluridine (cm5) modification of uridine bases located in the tRNA wobble position (U34). This priming modification represents the initial step for the subsequent formation of 5-carbamoylmethyl-uridine (ncm5U34) and 5-methoxycarbonylmethyl-uridine (mcm5U34) by other modification enzymes [6,7].
Charging the code — tRNA modification complexes
2019, Current Opinion in Structural BiologyCitation Excerpt :One of the chemically most complex modifications is catalyzed by a similarly complicated relay system. In eukaryotes, the highly conserved Elongator complex [62] carboxymethylates (cm5) 11 out of 13 yeast tRNAs carrying a U34 in the wobble position [63]. The core Elongator complex harbors two copies of each of its six subunits, Elp1-6 and displays an overall molecular weight of more than 850 kDa [64].
The emerging impact of tRNA modifications in the brain and nervous system
2019, Biochimica et Biophysica Acta - Gene Regulatory MechanismsCitation Excerpt :In some cases, ncm5U and mcm5U can be further methylated at the 2′-O-hydroxyl to yield 5-carbamoylmethyl-2-O-methyluridine (ncm5Um) or 5-methoxycarbonylmethyl-2′-O-methyluridine (mcm5Um). While the exact order of modification formation is unclear, the multi-subunit Elongator complex is required for early steps of mcm5U formation through the generation of cm5U and ncm5U (reviewed in [57,58]). Depending on the tRNA, the cm5U and/or ncm5U modification can then be further modified by the Trm9-Trm112 methyltransferase complex to yield mcm5U [59–63].
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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.