A large number of post-transcriptional base modifications in transfer RNAs have been described (Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (1998) Nucleic Acids Res. 26, 148-153). These modifications enhance and expand tRNA function to increase cell viability. The intermediates and genes essential for base modifications in many instances remain unclear. An example is wyebutosine (yW), a fluorescent tricyclic modification of an invariant guanosine situated on the 3'-side of the tRNA(Phe) anticodon. Although biosynthesis of yW involves several reaction steps, only a single pathway-specific enzyme has been identified (Kalhor, H. R., Penjwini, M., and Clarke, S. (2005) Biochem. Biophys. Res. Commun. 334, 433-440). We used comparative genomics analysis to identify a cluster of orthologous groups (COG0731) of wyosine family biosynthetic proteins. Gene knock-out and complementation studies in Saccharomyces cerevisiae established a role for YPL207w, a COG0731 ortholog that encodes an 810-amino acid polypeptide. Further analysis showed the accumulation of N(1)-methylguanosine (m(1)G(37)) in tRNA from cells bearing a YPL207w deletion. A similar lack of wyosine base and build-up of m(1)G(37) is seen in certain mammalian tumor cell lines. We proposed that the 810-amino acid COG0731 polypeptide participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
"It has been known for some time that the first step in Wye base formation is catalyzed by the m 1 G methyltransferase Trm5 (Droogmans and Grosjean 1987; Bjork et al. 2001). Recent work has shown that subsequent biosynthesis of wybutosine involves formation of the methyl imidazole ring by Tyw1 (Waas et al. 2005; Noma et al. 2006), followed by addition of the a-amino-a-carboxypropyl group of methionine by Tyw2 (Kalhor et al. 2005; Noma et al. 2006), and methylation of guanosine N3 by Tyw3 (Noma et al. 2006). Intriguingly, the last step of Wye base formation involves both methylation of the a-carboxy end group and methoxycarboxylation of the a-amino end group, with incorporation of carbon dioxide, all seemingly catalyzed by Tyw4 (Noma et al. 2006; Suzuki et al. 2009). "
[Show abstract][Hide abstract] ABSTRACT: tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis.
Genes & development 09/2010; 24(17):1832-60. DOI:10.1101/gad.1956510 · 10.80 Impact Factor
"Next, the tricyclic ring is formed from m 1 G37 by Tyw1 leading to imG-14 (fig. 1C) (Waas et al. 2005; Noma et al. 2006). Tyw1 is a radical S-Adenosyl-L-Methionine (S- AdoMet)-dependent [4Fe–4S] cluster containing enzyme using FMN as cofactor, but the exact mechanism of the reaction is unknown. "
[Show abstract][Hide abstract] ABSTRACT: Wyosine (imG) and its derivatives such as wybutosine (yW) are found at position 37 of phenylalanine-specific transfer RNA (tRNA(Phe)), 3' adjacent to the anticodon in Eucarya and Archaea. In Saccharomyces cerevisiae, formation of yW requires five enzymes acting in a strictly sequential order: Trm5, Tyw1, Tyw2, Tyw3, and Tyw4. Archaea contain wyosine derivatives, but their diversity is greater than in eukaryotes and the corresponding biosynthesis pathways still unknown. To identify these pathways, we analyzed the phylogenetic distribution of homologues of the yeast wybutosine biosynthesis proteins in 62 archaeal genomes and proposed a scenario for the origin and evolution of wyosine derivatives biosynthesis in Archaea that was partly experimentally validated. The key observations were 1) that four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya, 2) that the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. We also identified 7-aminocarboxypropyl-demethylwyosine (yW-86) and its N4-methyl derivative (yW-72) as final products in tRNAs of several Archaea when these were previously thought to be only intermediates of the eukaryotic pathway. We confirmed that isowyosine (imG2) and 7-methylwyosine (mimG) are two archaeal-specific guanosine-37 derivatives found in tRNA of both Euryarchaeota and Crenarchaeota. Finally, we proposed that the duplication of the trm5 gene in some Archaea led to a change in function from N1 methylation of guanosine to C7 methylation of 4-demethylwyosine (imG-14).
"Remarkably the output from the PLEX search showed only the two protein families exemplified by the yeast proteins Ypl207w and Ygl050w. Experimental validation by several groups has shown that both these proteins are, indeed, involved in wybutosine biosynthesis (Kalhor et al., 2005; Noma et al., 2006; Waas et al., 2005). The output from the NMPDR and MBGD, CoGenT+ + databases were less selective. "
[Show abstract][Hide abstract] ABSTRACT: As the molecular adapters between codons and amino acids, transfer-RNAs are pivotal molecules of the genetic code. The coding properties of a tRNA molecule do not reside only in its primary sequence. Posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. Despite a wealth of biophysical and structural knowledge of the tRNA modifications themselves, their pathways of biosynthesis had been until recently only partially characterized. This discrepancy was mainly due to the lack of obvious phenotypes for tRNA modification-deficient strains and to the difficulty of the biochemical assays used to detect tRNA modifications. However, the availability of hundreds of whole-genome sequences has allowed the identification of many of these missing tRNA-modification genes. This chapter reviews the methods that were used to identify these genes with a special emphasis on the comparative genomic approaches. Methods that link gene and function but do not rely on sequence homology will be detailed, with examples taken from the tRNA modification field.
Methods in Enzymology 02/2007; 425:153-83. DOI:10.1016/S0076-6879(07)25007-4 · 2.09 Impact Factor
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