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Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

ABSTRACT: Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

PROVIDER: PRJNA977562 | ENA |

REPOSITORIES: ENA

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Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

Project description:Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

| PRJNA996030 | ENA

Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

Project description:All elongator tRNAs harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Escherichia coli TrmA and TruB have both been shown to act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modification such as acp3U47 and 4-thiouridine. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the expression of many specific proteins is altered at the translational level. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation, and translation of specific genes thereby improving cellular fitness and explaining their conservation.

2024-06-05 | GSE237609 | GEO

Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

Project description:Abstract: tRNAs are highly modified in the elbow region and harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Although all elongator tRNAs contain these modifications across all domains of life, the cellular relevance of these modifications and their corresponding modifying enzymes remains elusive. In addition to modifying every tRNA, Escherichia coli TrmA and TruB have both been shown to fold tRNA independently of its modification activity acting as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. To identify how TrmA and TruB contribute to cellular fitness, we have systematically assessed the effects of deleting trmA and/or trmB in E. coli. Since tRNA folding is a pre-requisite for tRNA aminoacylation, we determined cellular aminoacylation levels revealing a global decrease in aminoacylation for all tRNAs in ΔtrmA and ΔtruB. Moreover, the absence of 5-methyluridine 54 or pseudouridine 55 alters tRNA modification at other positions: whereas acp3U47 is decreased, thiouridine levels are increased. Understanding the importance of TrmA and TruB for tRNA aminoacylation and modification, we then analyzed how these global tRNA changes in ΔtrmA and ΔtruB strains affect translation. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the abundances of many specific proteins are altered, and transcriptomics experiments suggest that the dysregulation of many proteins is controlled at the translational level. In conclusion, we demonstrate that universally conserved modifications of the tRNA elbow are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation and translation of specific genes thereby contributing to cellular fitness.

2023-05-31 | GSE233667 | GEO

Multi-environment fitness landscapes of a tRNA gene

Project description:A fitness landscape (FL) describes the genotype-fitness relationship in a given environment. To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently. Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments. Although genotype-by-environment interaction (G×E) is abundantly detected, its pattern is so simple that we can transform an existing FL to that in a new environment with fitness measures of only a few genotypes in the new environment. Under each environment, we observe prevalent, negatively biased epistasis between mutations (G×G). Epistasis-by-environment interaction (G×G×E) is also prevalent, but trends in epistasis difference between environments are predictable. Our study thus reveals simple rules underlying seemingly complex FLs, opening the door to understanding and predicting FLs in general.

2018-03-23 | GSE111508 | GEO

Multi-environment fitness landscapes of a tRNA gene

Project description:Multi-environment fitness landscapes of a tRNA gene

| PRJNA437246 | ENA

AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [liver]

Project description:The goal of this study was to determine the state of the tRNA transcriptome in Liver tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.

2019-11-08 | GSE140096 | GEO

AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [spleen]

Project description:The goal of this study was to determine the state of the tRNA transcriptome in Spleen tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.

2019-11-08 | GSE140095 | GEO

AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [Thymus]

Project description:The goal of this study was to determine the state of the tRNA transcriptome in Thymus tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.

2019-11-08 | GSE140094 | GEO

AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [brain]

Project description:The goal of this study was to determine the state of the tRNA transcriptome in Brain tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.

2019-11-08 | GSE140099 | GEO

AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [heart]

Project description:The goal of this study was to determine the state of the tRNA transcriptome in Heart tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.

2019-11-08 | GSE140098 | GEO

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