Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Nature Communications (Impact Factor: 11.47). 07/2012; 3:937. DOI: 10.1038/ncomms1938
Source: PubMed


Selective translation of survival proteins is an important facet of the cellular stress response. We recently demonstrated that this translational control involves a stress-specific reprogramming of modified ribonucleosides in tRNA. Here we report the discovery of a step-wise translational control mechanism responsible for survival following oxidative stress. In yeast exposed to hydrogen peroxide, there is a Trm4 methyltransferase-dependent increase in the proportion of tRNA(Leu(CAA)) containing m(5)C at the wobble position, which causes selective translation of mRNA from genes enriched in the TTG codon. Of these genes, oxidative stress increases protein expression from the TTG-enriched ribosomal protein gene RPL22A, but not its unenriched paralogue. Loss of either TRM4 or RPL22A confers hypersensitivity to oxidative stress. Proteomic analysis reveals that oxidative stress causes a significant translational bias towards proteins coded by TTG-enriched genes. These results point to stress-induced reprogramming of tRNA modifications and consequential reprogramming of ribosomes in translational control of cell survival.

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Available from: Madhu Dyavaiah, Mar 04, 2014
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    • "The condition employed in this study—a nonfermentable carbon source together with an elevated temperature—is known to lower tRNA transcription (Ciesla et al. 2007). Also, the general level of tRNA modification was reported to change upon oxidative stress, DNA damage or hydroxyl peroxide and temperature (Chan et al. 2010Chan et al. , 2012Alings et al. 2015). Furthermore, hypomodified tRNAs or tRNAs containing mutations that destabilize their structure were shown to be degraded at elevated temperatures via the RTD pathway (Chernyakov et al. 2008;Whipple et al. 2011). "
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    ABSTRACT: tRNA is essential for translation and decoding of the proteome. The yeast proteome responds to stress and tRNA biosynthesis contributes in this response by repression of tRNA transcription and alterations of tRNA modification. Here we report that the stress response also involves processing of pre-tRNA 3' termini. By a combination of Northern analyses and RNA sequencing, we show that upon shift to elevated temperatures and/or to glycerol-containing medium, aberrant pre-tRNAs accumulate in yeast cells. For pre-tRNAUAU (Ile) and pre-tRNAUUU (Lys) these aberrant forms are unprocessed at the 5' ends, but they possess extended 3' termini. Sequencing analyses showed that partial 3' processing precedes 5' processing for pre-tRNAUAU (Ile). An aberrant pre-tRNA(Tyr) that accumulates also possesses extended 3' termini, but it is processed at the 5' terminus. Similar forms of these aberrant pre-tRNAs are detected in the rex1Δ strain that is defective in 3' exonucleolytic trimming of pre-tRNAs but are absent in the lhp1Δ mutant lacking 3' end protection. We further show direct correlation between the inhibition of 3' end processing rate and the stringency of growth conditions. Moreover, under stress conditions Rex1 nuclease seems to be limiting for 3' end processing, by decreased availability linked to increased protection by Lhp1. Thus, our data document complex 3' processing that is inhibited by stress in a tRNA-type and condition-specific manner. This stress-responsive tRNA 3' end maturation process presumably contributes to fine-tune the levels of functional tRNA in budding yeast in response to environmental conditions.
    Full-text · Article · Jan 2016 · RNA
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    • "Since lack of modifications is often overcome by increased dosage of one or more of the unmodified tRNAs (Esberg, et al., 2006; Fernandez-Vazquez, et al., 2013; Guy, et al., 2012; Han, et al., 2015; Phizicky and Alfonzo, 2010), the numerous links between tRNA modifications and neurological defects suggest that the available pool of functional tRNAs may somehow be limited during development and function of the central nervous system, presumably leading to defects in translation or its regulation (Begley, et al., 2007; Chan, et al., 2012). The specific mechanisms by which defects in tRNA biology impact neurological function remain to be determined. "
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    ABSTRACT: tRNA modifications are crucial for efficient and accurate protein synthesis, and modification defects are frequently associated with disease. Yeast trm7Δ mutants grow poorly due to lack of 2'-O-methylated C32 (Cm32 ) and Gm34 on tRNA(Phe) , catalyzed by Trm7-Trm732 and Trm7-Trm734 respectively, which in turn results in loss of wybutosine at G37 . Mutations in human FTSJ1, the likely TRM7 homolog, cause non-syndromic X-linked intellectual disability (NSXLID), but the role of FTSJ1 in tRNA modification is unknown. Here we report that tRNA(Phe) from two genetically independent cell lines of NSXLID patients with loss of function FTSJ1 mutations nearly completely lacks Cm32 and Gm34 , and has reduced peroxywybutosine (o2yW37 ). Additionally, tRNA(Phe) from an NSXLID patient with a novel FTSJ1-p.A26P missense allele specifically lacks Gm34 , but has normal levels of Cm32 and o2yW37 . tRNA(Phe) from the corresponding Saccharomyces cerevisiae trm7-A26P mutant also specifically lacks Gm34 , and the reduced Gm34 is not due to weaker Trm734 binding. These results directly link defective 2'-O-methylation of the tRNA anticodon loop to FTSJ1 mutations, suggest that the modification defects cause NSXLID, and may implicate Gm34 of tRNA(Phe) as the critical modification. These results also underscore the widespread conservation of the circuitry for Trm7-dependent anticodon loop modification of eukaryotic tRNA(Phe) . This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Full-text · Article · Aug 2015 · Human Mutation
    • "With purified RNA in hand, the next step is to hydrolyze the RNA into oligonucleotide fragments or individual ribonucleotides, with the latter dephosphorylated to ribonucleoside form for LC–MS analysis. The oligonucleotides are used for localizing and quantifying modified ribonucleosides in specific tRNA species (Castleberry & Limbach, 2010; Chan et al., 2012; Hossain & Limbach, 2007), while the ribonucleosides can be identified and quantified by LC–MS as discussed later in this chapter. We focus here on the hydrolysis of RNA into ribonucleosides for analysis of stress-induced changes and patterns in translational response mechanisms. "
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    ABSTRACT: Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications. © 2015 Elsevier Inc. All rights reserved.
    No preview · Article · Aug 2015 · Methods in enzymology
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