Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae

Johansson, Marcus J O; Byström, Andeŕs S.

doi:10.1007/b105814

Cited by 30 publications

(39 citation statements)

References 156 publications

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“…6D). Since the only Mod5p substrate whose gene encodes A in position 34, tRNA Ser AGA , contains inosine (I) at this position (Zachau et al 1966;in Johansson and Bystrom 2005), we also examined ASLs with I34. The ASL with I34 was relatively inactive for both proteins (Fig.…”

Section: Substrate Specificity Of Tit1pmentioning

confidence: 99%

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Lamichhane¹,

Blewett²,

Maraia³

2011

RNA

139

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The N 6 -(isopentenyl)adenosine (i 6 A) modification of some tRNAs at position A37 is found in all kingdoms and facilitates codonspecific mRNA decoding, but occurs in different subsets of tRNAs in different species. Here we examine yeasts' tRNA isopentenyltransferases (i.e., dimethylallyltransferase, DMATase, members of the D 2 -isopentenylpyrophosphate transferase, IPPT superfamily) encoded by tit1 + in Schizosaccharomyces pombe and MOD5 in Saccharomyces cerevisiae, whose homologs are Escherichia coli miaA, the human tumor suppressor TRIT1, and the Caenorhabditis elegans life-span gene product GRO-1. A major determinant of miaA activity is known to be the single-stranded tRNA sequence, A36A37A38, in a stem-loop. tRNA Trp CCA from either yeast is a Tit1p substrate, but neither is a Mod5p substrate despite the presence of A36A37A38. We show that Tit1p accommodates a broader range of substrates than Mod5p. tRNA Trp CCA is distinct from Mod5p substrates, which we sort into two classes based on the presence of G at position 34 and other elements. A single substitution of C34 to G converts tRNA Trp CCA to a Mod5p substrate in vitro and in vivo, consistent with amino acid contacts to G34 in existing Mod5p-tRNA Cys GCA crystal structures. Mutation of Mod5p in its G34 recognition loop region debilitates it differentially for its G34 (class I) substrates. Multiple alignments reveal that the G34 recognition loop sequence of Mod5p differs significantly from Tit1p, which more resembles human TRIT1 and other DMATases. We show that TRIT1 can also modify tRNA Trp CCA consistent with broad recognition similar to Tit1p. This study illustrates previously unappreciated molecular plasticity and biological diversity of the tRNA-isopentenyltransferase system of eukaryotes.

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Section: Substrate Specificity Of Tit1pmentioning

confidence: 99%

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Lamichhane¹,

Blewett²,

Maraia³

2011

RNA

139

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“…Ribosomal RNA methylation sites are clustered in functional regions of the ribosome, including the peptidyl transferase center and the tRNA binding sites (A/P/E), and have been shown to be important for ribosome assembly, structural stability, and translational accuracy (Piekna-Przybylska et al 2008;Baudin-Baillieu et al 2009). Methylation of tRNAs and elongation and release factors modulates translational accuracy and translation termination efficiency (Johansson and Byström 2005;Polevoda and Sherman 2007;Dzialo et al 2014;Hori 2014). Ribosomal proteins are methylated in the three kingdoms of life, but little is known about the physiological roles of these modifications (Arnold and Reilly 1999;Lee et al 2002;Odintsova et al 2003;Yu et al 2005;Polevoda and Sherman 2007;Nesterchuk et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

Al-Hadid

Roy

Chanfreau

et al. 2016

RNA

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Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae. Histidine 243 lies close to the peptidyl transferase center in a functionally important region of Rpl3 designated as the basic thumb that coordinates the decoding, peptidyl transfer, and translocation steps of translation elongation. Hpm1 was recently implicated in ribosome biogenesis and translation. However, the biological role of methylation of its Rpl3 substrate has not been identified. Here we interrogate the role of Rpl3 methylation at H243 by investigating the functional impact of mutating this histidine residue to alanine (rpl3-H243A). Akin to Hpm1-deficient cells, rpl3-H243A cells accumulate 35S and 23S pre-rRNA precursors to a similar extent, confirming an important role for histidine methylation in pre-rRNA processing. In contrast, Hpm1-deficient cells but not rpl3-H243A mutants show perturbed levels of ribosomal subunits. We show that Hpm1 has multiple substrates in different subcellular fractions, suggesting that methylation of proteins other than Rpl3 may be important for controlling ribosomal subunit levels. Finally, translational fidelity assays demonstrate that like Hpm1-deficient cells, rpl3-H243A mutants have defects in translation elongation resulting in decreased translational accuracy. These data suggest that Rpl3 methylation at H243 is playing a significant role in translation elongation, likely via the basic thumb, but has little impact on ribosomal subunit levels. Hpm1 is therefore a multifunctional methyltransferase with independent roles in ribosome biogenesis and translation.

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“…To the right of each tRNA, the modification at positions 34 (the wobble position) is shown. Data compiled from Johansson and Byström (2005 The bacterial TtcA protein, which is required for the synthesis of s 2 C at position 32 of a subset of tRNAs in Escherichia coli, belongs to a protein family with members from all three phylogenetic domains (Jäger et al 2004). These proteins can be divided into two phylogenetic groups, where bacterial TtcA homologs are in Group 1 and eukaryotic and archaeal homologs are in Group 2 (Fig.…”

Section: Introductionmentioning

confidence: 99%

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

Björk

Huang²,

Persson³

et al. 2007

RNA

Self Cite

178

211

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Transfer RNAs specific for Gln, Lys, and Glu from all organisms (except Mycoplasma) and organelles have a 2-thiouridine derivative (xm 5 s 2 U) as wobble nucleoside. These tRNAs read the A-and G-ending codons in the split codon boxes His/Gln, Asn/Lys, and Asp/Glu. In eukaryotic cytoplasmic tRNAs the conserved constituent (xm 5 -) in position 5 of uridine is 5-methoxycarbonylmethyl (mcm 5 ). A protein (Tuc1p) from yeast resembling the bacterial protein TtcA, which is required for the synthesis of 2-thiocytidine in position 32 of the tRNA, was shown instead to be required for the synthesis of 2-thiouridine in the wobble position (position 34). Apparently, an ancient member of the TtcA family has evolved to thiolate U34 in tRNAs of organisms from the domains Eukarya and Archaea. Deletion of the TUC1 gene together with a deletion of the ELP3 gene, which results in the lack of the mcm 5 side chain, removes all modifications from the wobble uridine derivatives of the cytoplasmic tRNAs specific for Gln, Lys, and Glu, and is lethal to the cell. Since excess of the unmodified form of these three tRNAs rescued the double mutant elp3 tuc1, the primary function of mcm 5 s 2 U34 seems to be to improve the efficiency to read the cognate codons rather than to prevent mis-sense errors. Surprisingly, overexpression of the mcm 5 s 2 U-lacking tRNA Lys alone was sufficient to restore viability of the double mutant.

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Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae

Cited by 30 publications

References 156 publications

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

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

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Transfer RNA modifications and modifying enzymes in Saccharomyces cerevisiae

Cited by 30 publications

References 156 publications

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

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

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