Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism

Selvadurai, Kiruthika; Wang, Pei; Seimetz, Joseph; Huang, Raven H.

doi:10.1038/nchembio.1610

Cited by 95 publications

(132 citation statements)

References 23 publications

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“…Nevertheless, the detailed chemistry of the Elongator modification reaction is insufficiently described, and the role of the resulting modifications is not fully understood 11, 12, 13. In particular, it is currently unclear how tRNA is delivered to the active center and how the high modification turnover can be achieved in the context of the full complex.…”

Section: Introductionmentioning

confidence: 99%

Architecture of the yeast Elongator complex

et al. 2016

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The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1‐6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub‐complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two‐lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.

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Section: Introductionmentioning

confidence: 99%

Architecture of the yeast Elongator complex

et al. 2016

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“…17 Additional support for a role in tRNA modification was recently strengthened by the observation that the Elp3p homolog from the archaea Methanocaldococcus infernus in vitro modifies U 34 in tRNA to cm 5 U in the presence of acetyl-CoA. 24 In Yeast, The Phenotypes of Elongator Deficient Cells are Linked to tRNA Modification…”

Section: 15mentioning

confidence: 99%

“…51 Homologues to the Elp3 protein are found in essentially all archaea but not the other subunits of the Elongator complex. 24,51 This suggests that archaea require only Elp3p for formation of cm 5 U. In vitro, recombinant Elp3p from Methanocaldococcus infernus catalyze the transfer of an acetyl radical forming cm 5 U in the presence of acetyl-CoA, the reducing agent sodium dithionite and Sadenosylmethionine.…”

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confidence: 99%

“…In vitro, recombinant Elp3p from Methanocaldococcus infernus catalyze the transfer of an acetyl radical forming cm 5 U in the presence of acetyl-CoA, the reducing agent sodium dithionite and Sadenosylmethionine. 24 Thus, this unique enzymatic reaction mechanism explains the requirement of the SAM and HAT domains in Elp3p. The last step in formation of mcm 5 U requires the tRNA methyltransferase Trm9 and the Trm112 protein, whereas no gene product responsible for the last step in formation of ncm 5 U is known (Fig.…”

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confidence: 99%

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Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes

Karlsborn

Tükenmez

Mahmud³

et al. 2014

RNA Biology

100

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“…These findings and studies [which demonstrate the association of the Elongator complex with the RNA polymerase II (RNAPII) holoenzyme, its ability to bind to nascent pre-mRNA, and the facilitation of RNAPII transcripts through chromatin in an acetyl-CoA-dependent manner] support its role in transcriptional regulation (7,9,17). In addition to its participation in transcriptional regulation, the Elongator complex may also play a pivotal role in the regulation of translation through its direct effect on tRNA modification, from archaeal organisms to mammals (18)(19)(20)(21)(22).Coincident with the dual roles of Elongator in transcriptional and translational regulation, it has been shown that several genes involved in cell migration and a few meiotic genes during spermatogenesis were down-regulated in FD-derived fibroblasts (23) and in mouse upon Elp1 depletion (22), respectively, and that several genes involved in oligodendrocyte development and myelin formation were down-regulated both in the cerebrum of FD patients (24) and in an FD mouse model (25). Recently, Frances Lefcort and coworkers discovered that Elp1 is essential for the genesis of tropomyosinrelated kinase A nociceptors and thermoreceptors in mice (26).…”

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confidence: 99%

Dimerization of elongator protein 1 is essential for Elongator complex assembly

Lin

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The evolutionarily conserved Elongator complex, which is composed of six subunits elongator protein 1 (Elp1 to -6), plays vital roles in gene regulation. The molecular hallmark of familial dysautonomia (FD) is the splicing mutation of Elp1 [also known as IκB kinase complex-associated protein (IKAP)] in the nervous system that is believed to be the primary cause of the devastating symptoms of this disease. Here, we demonstrate that disease-related mutations in Elp1 affect Elongator assembly, and we have determined the structure of the C-terminal portion of human Elp1 (Elp1-CT), which is sufficient for full-length Elp1 dimerization, as well as the structure of the cognate dimerization domain of yeast Elp1 (yElp1-DD). Our study reveals that the formation of the Elp1 dimer contributes to its stability in vitro and in vivo and is required for the assembly of both the human and yeast Elongator complexes. Functional studies suggest that Elp1 dimerization is essential for yeast viability. Collectively, our results identify the evolutionarily conserved dimerization domain of Elp1 and suggest that the pathological mechanisms underlying the onset and progression of Elp1 mutation-related disease may result from impaired Elongator activities.F amilial dysautonomia (FD) (Online Mendelian Inheritance in Man: 223900), which is an Ashkenazi Jewish disorder with an incidence of 1:3,700 live births, is an autosomal recessive disorder that affects the development and survival of sensory, sympathetic, and some parasympathetic neurons (1). FD patients are characterized by cardiovascular instability, gastrointestinal dysfunction, vomiting crises, decreased sensitivity to pain and temperature, and recurrent pneumonias (2). The most common mutation, which represents >99.5% of all FD patients, is a T-to-C transition in position six of the donor splice site of intron 20 in the gene transcript of the IκB kinase (IKK) complex-associated protein (IKAP), also known as elongator protein 1 (Elp1) (3, 4). This splicing mutation causes skipping of exon 20 and results in encoding a truncated IKAP/Elp1 protein (referred to as Elp1-FD hereafter) (Fig. 1A).IKAP/Elp1 was originally identified as a scaffold protein and a regulator for IKKs involved in proinflammatory cytokine signaling (5). However, contrary to this observation, subsequent analyses failed to demonstrate an association with IKKs (6). Coincident and subsequent studies supported the notion that IKAP/Elp1 is a component of the highly conserved Elongator complex from different species (7-9) (for simplicity, the term Elp1 will be used in the following discussion). The holo-Elongator complex contains six subunits (Elp1 to -6) and assembles into a core subcomplex (Elp1 to -3) and an accessory subcomplex (Elp4 to -6), which is involved in substrate recognition (10, 11). Moreover, the holo-Elongator is a functional unit, as illustrated in yeast, in which strains lacking any of the six Elp proteins exhibit similar phenotypes (7,12,13), and in that the removal of any Elongator subunits affects the...

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Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism

Cited by 95 publications

References 23 publications

Architecture of the yeast Elongator complex

Architecture of the yeast Elongator complex

Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes

Dimerization of elongator protein 1 is essential for Elongator complex assembly

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