Elongator Complex Influences Telomeric Gene Silencing and DNA Damage Response by Its Role in Wobble Uridine tRNA Modification

Abstract

Elongator complex is required for formation of the side chains at position 5 of modified nucleosides 5-carbamoylmethyluridine (ncm5U34), 5-methoxycarbonylmethyluridine (mcm5U34), and 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34) at wobble position in tRNA. These modified nucleosides are important for efficient decoding during translation. In a recent publication, Elongator complex was implicated to participate in telomeric gene silencing and DNA damage response by interacting with proliferating cell nuclear antigen (PCNA). Here we show that elevated levels of tRNALys s2 UUU, tRNAGln s2 UUG, and tRNAGlu s2 UUC, which in a wild-type background contain the mcm5s2U nucleoside at position 34, suppress the defects in telomeric gene silencing and DNA damage response observed in the Elongator mutants. We also found that the reported differences in telomeric gene silencing and DNA damage response of various elp3 alleles correlated with the levels of modified nucleosides at U34. Defects in telomeric gene silencing and DNA damage response are also observed in strains with the tuc2Δ mutation, which abolish the formation of the 2-thio group of the mcm5s2U nucleoside in tRNALys mcm5s2UUU, tRNAGln mcm5s2UUG, and tRNAGlu mcm5s2UUC. These observations show that Elongator complex does not directly participate in telomeric gene silencing and DNA damage response, but rather that modified nucleosides at U34 are important for efficient expression of gene products involved in these processes. Consistent with this notion, we found that expression of Sir4, a silent information regulator required for assembly of silent chromatin at telomeres, was decreased in the elp3Δ mutants.

Protein folding and tRNA biology

“…BElongator^, a multimeric protein complex with methyl-transferase activity, participates in the first steps. BElongator^is also related to other cellular processes, such as elongation by RNA polymerase II, histone acetylation, telomeric gene silencing, and DNA repair (Chen et al 2011;Karlsborn et al 2014). Noteworthy in yeast, the phenotype produced by a defective U34 modification (morphological and growth alterations) was reverted by the overexpression of the involved tRNA (Klassen et al 2016b).…”

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

“…Alterations of other modifications at position 34 such as ncm 5 Um 34 result in sensitivity to the aminoglycoside antibiotic paromomycin that causes misreading of near cognate codons (Kalhor and Clarke 2003). Some of the subunits of the enzyme responsible for ncm 5 Um 34 and ncm 5 s 2 U 34 modification were previously identified as components of the elongator complex that functions in transcriptional elongation, silencing at telomeres, and DNA damage response; it since has been shown that the phenotypes are indirect consequences of wobble position errors in translation of proteins that function in these processes (Chen et al 2011). Similarly, mutations of genes encoding proteins of the KEOPS complex cause growth defects and telomere shortening.…”

Glutaredoxin GRXS17 Associates with the Cytosolic Iron-Sulfur Cluster Assembly Pathway

“…The mcm 5 modification is catalyzed by the elongator (ELP) pathway and requires the Elp3/ELO3 catalytic subunit, i.e. a [4Fe-4S] protein Paraskevopoulou et al, 2006;Selvadurai et al, 2014), together with the Trm9/Trm112 complex, which is a tRNA methyltransferase necessary for the last step of mcm 5 formation (Kalhor and Clarke, 2003;Chen et al, 2011;Leihne et al, 2011). The presence of the mcm 5 chain is necessary for an effective thiolation of tRNAs (Leidel et al, 2009;Chen et al, 2011).…”

“…Although in vivo data are scarce, tRNA modifications might have a regulatory function, because certain open reading frames (ORFs) are enriched in codons recognized by modified tRNAs. In yeast, genes involved in the DNA-damage response are enriched in GAA, AAA, and CAA codons and elongator mutants defective in mcm 5 s 2 modification are hypersensitive to DNA stress (Chen et al, 2011).…”