Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

Patil, Ashish; Dyavaiah, Madhu; Joseph, Fraulin; Rooney, John P.; Chan, Ching-Kit; Dedon, Peter C.; Begley, Thomas J.

doi:10.4161/cc.21919

Cited by 75 publications

(88 citation statements)

References 42 publications

(69 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Undermodified tRNAs contribute to translational errors and ϩ1 translational frameshifting (25,(28)(29)(30)(31). Recent reports suggest that the Trm9-catalyzed mcm 5 U34 (wobble position) tRNA modification may act in a regulatory manner in eukaryotic cells, influencing eukaryotic cell cycle progression in response to DNA damage and oxidative stress, stimulating the eukaryotic heat shock and unfolded protein responses, and perturbing cellular signaling (32)(33)(34)(35)(36). Given these observations, it is likely that tRNA modifications play a regulatory role in prokaryotic physiology as well.…”

Section: R Pos (mentioning

confidence: 99%

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

Thompson

Gottesman

2014

J Bacteriol

View full text Add to dashboard Cite

The stationary phase/general stress response sigma factor RpoS ( S ) is necessary for adaptation and restoration of homeostasis in stationary phase. As a physiological consequence, its levels are tightly regulated at least at two levels. Multiple small regulatory RNA molecules modulate its translation, in a manner that is dependent on the RNA chaperone Hfq and the rpoS 5= untranslated region. ClpXP and the RssB adaptor protein degrade RpoS, unless it is protected by an anti-adaptor. We here find that, in addition to these posttranscriptional levels of regulation, tRNA modification also affects the steady-state levels of RpoS. We screened mutants of several RNA modification enzymes for an effect on RpoS expression and identified the miaA gene, encoding a tRNA isopentenyltransferase, as necessary for full expression of both an rpoS750-lacZ translational fusion and the RpoS protein. This effect is independent of rpoS, the regulatory RNAs, and RpoS degradation. RpoD steady-state levels were not significantly different in the absence of MiaA, suggesting that this is an RpoS-specific effect. The rpoS coding sequence is significantly enriched for leu codons that use MiaA-modified tRNAs, compared to rpoD and many other genes. Dependence on MiaA may therefore provide yet another way for RpoS levels to respond to growth conditions.

show abstract

Section: R Pos (mentioning

confidence: 99%

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

Thompson

Gottesman

2014

J Bacteriol

View full text Add to dashboard Cite

show abstract

“…An emerging theme has been that tRNA modifications are intimately involved in cellular stress response. For example, the deficiency of Trm9 affects cellular response to DNA damage, because translation of damage response genes requires Trm9-dependent tRNA modification for the last step of synthesis of mcm 5 U34 in tRNA Arg/UCU and mcm 5 s 2 U34 in tRNA Glu/UUC (30,31). Similarly, the deficiency of Trm4 affects cellular response to oxidative stress, because translation of stress-response genes requires Trm4-dependent methylation in m 5 C34 of tRNA Leu/CAA (32).…”

mentioning

confidence: 99%

The Temperature Sensitivity of a Mutation in the Essential tRNA Modification Enzyme tRNA Methyltransferase D (TrmD)

Masuda

Sakaguchi²,

Liu³

et al. 2013

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Although temperature-sensitive (ts) mutations of TrmD exist, deficient in converting G37-to m 1 G37-tRNA, the basis of their phenotype is unknown. Results:The ts-S88L mutation, while conferring thermal lability, caused a stronger defect on catalysis. Conclusion:The catalytic defect of the ts-S88L mutation reduced the quantity and quality of tRNA methylation. Significance: ts mutations leading to catalytic defects are useful for studying enzyme mechanism.Conditional temperature-sensitive (ts) mutations are important reagents to study essential genes. Although it is commonly assumed that the ts phenotype of a specific mutation arises from thermal denaturation of the mutant enzyme, the possibility also exists that the mutation decreases the enzyme activity to a certain level at the permissive temperature and aggravates the negative effect further upon temperature upshifts. Resolving these possibilities is important for exploiting the ts mutation for studying the essential gene. The trmD gene is essential for growth in bacteria, encoding the enzyme for converting G37 to m 1 G37 on the 3 side of the tRNA anticodon. This conversion involves methyl transfer from S-adenosyl methionine and is critical to minimize tRNA frameshift errors on the ribosome. Using the ts-S88L mutation of Escherichia coli trmD as an example, we show that although the mutation confers thermal lability to the enzyme, the effect is relatively minor. In contrast, the mutation decreases the catalytic efficiency of the enzyme to 1% at the permissive temperature, and at the nonpermissive temperature, it renders further deterioration of activity to 0.1%. These changes are accompanied by losses of both the quantity and quality of tRNA methylation, leading to the potential of cellular pleiotropic effects. This work illustrates the principle that the ts phenotype of an essential gene mutation can be closely linked to the catalytic defect of the gene product and that such a mutation can provide a useful tool to study the mechanism of catalytic inactivation.Essential genes encode critical cellular functions that are not supported by redundant pathways. Because of their indispensability, essential genes have been studied and functionally controlled by using temperature-sensitive (ts) 4 alleles. Such alleles are typically mis-sense mutations, which preserve the gene function at permissive and low temperatures but inactivate the gene function upon temperature upshifts. The study of ts phenotypes is fundamental and important for insight into gene essentiality. However, the molecular basis of ts phenotypes of essential genes remains poorly understood; although it is generally assumed that such phenotypes result from thermal inactivation of gene products, the possibility that they arise from inherent functional defects that become lethal at higher temperatures is often overlooked. In the latter case, ts mutations giving rise to severe functional defects at the permissive temperature can be powerful tools to study essential genes and to correlate pheno...

show abstract

“…There are a host of tRNA modifications that are most crucial in translational frameshift suppression and the majority of them reside within the anticodon stem-loop (ASL), flanking the anticodon at positions 34 and 37, including 5-methyluridine (m 5 U34), 5-methylcytidine (m 5 C34), and N 6 -isopentenyladenosine (i 6 A37) (Endres et al 2015). Certain tRNA modifications act in a regulatory manner on physiological circuits within the cell, such as DNA damage and oxidative stress in eukaryotic cells (Begley et al 2007;Chan et al 2010Chan et al , 2012Patil et al 2012;Lamichhane et al 2013a). There is limited information on the regulatory role of tRNA modifications in bacterial cells.…”

Section: Introductionmentioning

confidence: 99%

The i⁶A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation

Aubee

Olu

Thompson

2016

RNA

View full text Add to dashboard Cite

The translation of rpoS (σ S ), the general stress/stationary phase sigma factor, is tightly regulated at the post-transcriptional level by several factors via mechanisms that are not clearly defined. One of these factors is MiaA, the enzyme necessary for the first step in the N 6 -isopentyl-2-thiomethyladenosinemethyladenosine 37 (ms 2 i 6 A37) tRNA modification. We tested the hypothesis that an elevated UUX-Leucine/total leucine codon ratio can be used to identify transcripts whose translation would be sensitive to loss of the MiaA-dependent modification. We identified iraP as another candidate MiaA-sensitive gene, based on the UUX-Leucine/ total leucine codon ratio. An iraP-lacZ fusion was significantly decreased in the absence of MiaA, consistent with our predictive model. To determine the role of MiaA in UUX-Leucine decoding in rpoS and iraP, we measured β-galactosidasespecific activity of miaA − rpoS and iraP translational fusions upon overexpression of leucine tRNAs. We observed suppression of the MiaA effect on rpoS, and not iraP, via overexpression of tRNA LeuX but not tRNA LeuZ . We also tested the hypothesis that the MiaA requirement for rpoS and iraP translation is due to decoding of UUX-Leucine codons within the rpoS and iraP transcripts, respectively. We observed a partial suppression of the MiaA requirement for rpoS and iraP translational fusions containing one or both UUX-Leucine codons removed. Taken together, this suggests that MiaA is necessary for rpoS and iraP translation through proper decoding of UUX-Leucine codons and that rpoS and iraP mRNAs are both modification tunable transcripts (MoTTs) via the presence of the modification.

show abstract

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

Cited by 75 publications

References 42 publications

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

The Temperature Sensitivity of a Mutation in the Essential tRNA Modification Enzyme tRNA Methyltransferase D (TrmD)

The i⁶A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation

Contact Info

Product

Resources

About

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

Cited by 75 publications

References 42 publications

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

The MiaA tRNA Modification Enzyme Is Necessary for Robust RpoS Expression in Escherichia coli

The Temperature Sensitivity of a Mutation in the Essential tRNA Modification Enzyme tRNA Methyltransferase D (TrmD)

The i6A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation

Contact Info

Product

Resources

About

The i⁶A37 tRNA modification is essential for proper decoding of UUX-Leucine codons during rpoS and iraP translation