Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.

Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA.
Genes & Development (Impact Factor: 12.64). 06/2008; 22(10):1369-80. DOI: 10.1101/gad.1654308
Source: PubMed

ABSTRACT Mature tRNA is normally extensively modified and extremely stable. Recent evidence suggests that hypomodified mature tRNA in yeast can undergo a quality control check by a rapid tRNA decay (RTD) pathway, since mature tRNA(Val(AAC)) lacking 7-methylguanosine and 5-methylcytidine is rapidly degraded and deacylated at 37 degrees C in a trm8-Delta trm4-Delta strain, resulting in temperature-sensitive growth. We show here that components of this RTD pathway include the 5'-3' exonucleases Rat1 and Xrn1, and Met22, which likely acts indirectly through Rat1 and Xrn1. Since deletion of MET22 or mutation of RAT1 and XRN1 prevent both degradation and deacylation of mature tRNA(Val(AAC)) in a trm8-Delta trm4-Delta strain and result in healthy growth at 37 degrees C, hypomodified tRNA(Val(AAC)) is at least partially functional and structurally intact under these conditions. The integrity of multiple mature tRNA species is subject to surveillance by the RTD pathway, since mutations in this pathway also prevent degradation of at least three other mature tRNAs lacking other combinations of modifications. The RTD pathway is the first to be implicated in the turnover of mature RNA species from the class of stable RNAs. These results and the results of others demonstrate that tRNA, like mRNA, is subject to multiple quality control steps.

  • [Show abstract] [Hide abstract]
    ABSTRACT: ABSTRACT tRNA modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. There are seven cytoplasmic tRNA modifications in the yeast Saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, five of which require only a single subunit in bacteria, and two of which are not found in bacteria. These enzymes include the deaminase Tad2-Tad3, and the methyltransferases Trm6-Trm61, Trm8-Trm82, Trm7-Trm732, and Trm7-Trm734, Trm9-Trm112, and Trm11-Trm112. We describe the occurrence and biological role of each modification, evidence for a required partner protein in S. cerevisiae and other eukaryotes, evidence for a single subunit in bacteria, and evidence for the role of the non-catalytic binding partner. Although it is unclear why these eukaryotic enzymes require partner proteins, studies of some two-subunit modification enzymes suggest that the partner proteins help expand substrate range or allow integration of cellular activities.
    RNA biology. 01/2015;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Beyond their central role in protein synthesis, transfer RNAs (tRNAs) have many other crucial functions. This includes various roles in the regulation of gene expression, stress responses, metabolic processes and priming reverse transcription. In the RNA world, tRNAs are, with ribosomal RNAs, among the most stable molecules. Nevertheless, they are not eternal. As key elements of cell function, tRNAs need to be continuously quality-controlled. Two tRNA surveillance pathways have been identified. They act on hypo-modified or mis-processed pre-tRNAs and on mature tRNAs lacking modifications. A short overview of these two pathways will be presented here. Furthermore, while the exoribonucleases acting in these pathways ultimately lead to complete tRNA degradation, numerous tRNA-derived fragments (tRFs) are present within a cell. These cleavage products of tRNAs now potentially emerge as a new class of small non-coding RNAs (sncRNAs) and are suspected to have important regulatory functions. The tRFs are evolutionarily widespread and created by cleavage at different positions by various endonucleases. Here, we review our present knowledge on the biogenesis and function of tRFs in various organisms.
    International Journal of Molecular Sciences 16(1):1873-1893. · 2.46 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Trm4p from Saccharomyces cerevisiae and its mammalian orthologue Nsun2 fabricate 5-methylcytosine (m(5)C) in RNA molecules utilizing a dual-cysteine catalytic mechanism. These enzymes are now shown to form covalent complexes with previously methylated RNA. Enzyme linkage to methylated RNA requires S-adenosylhomocysteine (AdoHcy), and the removal of this metabolite results in the disassembly of preexisting complexes. The fraction of Trm4p linked to modified RNA is influenced by the AdoHcy concentration and by the pH of the solution, with maximal formation of Trm4p-RNA complexes observed in the pH range of 5.5-6.5. Four active-site residues critical for Trm4p-mediated tRNA methylation are also required for the formation of the denaturant-resistant complexes with m(5)C-containing RNA. On the basis of these findings, it is proposed that formation of a covalent complex between dual-cysteine RNA:m(5)C methyltransferases and methylated RNA provides a unique means by which metabolic factors can influence RNA. By controlling the degree of formation of the enzyme-RNA covalent complex, AdoHcy and pH are likely to influence the extent of m(5)C formation and the rate of release of methylated RNA from RNA:m(5)C methyltransferases. Metabolite-induced covalent complexes could plausibly affect the processing and function of m(5)C-containing RNAs.
    Biochemistry 11/2014; · 3.38 Impact Factor


1 Download
Available from