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: 10.8). 06/2008; 22(10):1369-80. DOI: 10.1101/gad.1654308
Source: PubMed


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.

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    • "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). In addition , heat shock as well as methionine starvation, or oxidative stress, caused tRNA cleavage in the anticodon loop by Rny1, creating tRNA halves (Thompson et al. 2008;Thompson and Parker 2009). "
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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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    • "In the yeast Saccharomyces cerevisiae, mutations affecting 16 of the 25 tRNA modifications lead to distinct phenotypes, including lethality for three mutants, and poor growth or temperature sensitivity for six other mutants (Hopper, 2013). Modifications in and around the tRNA anticodon loop (residues 31-39) are particularly important in all organisms (de Crecy-Lagard, et al., 2012), often affecting decoding (Agris, et al., 2007; Murphy, et al., 2004), charging by the cognate tRNA aminoacyl synthetase (Muramatsu, et al., 1988; Putz, et al., 1994), and/or frame maintenance (Bekaert and Rousset, 2005; Urbonavicius, et al., 2001; Waas, et al., 2007), whereas modifications in the body of the tRNA often contribute to folding or stability (Hall, et al., 1989; Helm, et al., 1999; Whipple, et al., 2011; Yue, et al., 1994) and are required to avoid decay by two known degradation pathways (Alexandrov, et al., 2006; Chernyakov, et al., 2008; Kadaba, et al., 2004; Kadaba, et al., 2006; LaCava, et al., 2005; Schneider, et al., 2007; Vanacova, et al., 2005). "
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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
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    • "What, then, do tRNA modifications contribute to the process of gene expression? Lack of modifications in the body of tRNAs can result in defects in aminoacylation and rapid degradation of hypomodified tRNAs (Alexandrov et al., 2006; Chernyakov et al., 2008; Whipple et al., 2011; Tuorto et al., 2012). Modifications at or near the anticodon appear to affect translation directly by mediating codon–anticodon interactions and facilitating accurate and efficient translation of the genetic code (Yarian, 2002; Murphy et al., 2004; Agris et al., 2007). "
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    ABSTRACT: Although tRNA modifications have been well catalogued, the precise functions of many modifications and their roles in mediating gene expression are still being elucidated. While tRNA modifications were long assumed to be constitutive, it is now apparent that the modification status of tRNAs changes in response to different environmental conditions. The URM1 pathway is required for thiolation of the cytoplasmic tRNAs tGlu(UUC), tGln(UUG) and tLys(UUU) in Saccharomyces cerevisiae. We demonstrate that URM1 pathway mutants have impaired translation, which results in increased basal activation of the Hsf1-mediated heat shock response; we also find that tRNA thiolation levels in wild type cells decrease when cells are grown at elevated temperature. We show that defects in tRNA thiolation can be conditionally advantageous, conferring resistance to endoplasmic reticulum stress. URM1 pathway proteins are unstable, and hence are more sensitive to changes in the translational capacity of cells, which is decreased in cells experiencing stresses. We propose a model in which a stress-induced decrease in translation results in decreased levels of URM1 pathway components, which results in decreased tRNA thiolation levels, which further serves to decrease translation. This mechanism ensures that tRNA thiolation and translation are tightly coupled and coregulated according to need.
    Full-text · Article · Nov 2014 · Molecular Biology of the Cell
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