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

Chan, Ching-Kit; Pang, Yan; Deng, Wenjun; Babu, I. Ramesh; Dyavaiah, Madhu; Begley, Thomas J.; Dedon, Peter C.

doi:10.1038/ncomms1938

Cited by 379 publications

(490 citation statements)

References 48 publications

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“…Recently, codon usage bias has been observed to influence cell cycle development (24), the responses of the cell to stress-specific conditions (25,26), and protein phosphorylation profile and stability (27). In addition, it was discovered that silent mutations could cause serious diseases (10) or affect frameshift in a given organism (28).…”

Section: Discussionmentioning

confidence: 99%

Genetic Code-guided Protein Synthesis and Folding in Escherichia coli

Wang

Cai

et al. 2013

Journal of Biological Chemistry

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Background: Synonymous codon usage affects protein properties in a given organism. Results: A total of 342 antibody codon variants were identified, differing significantly in solubility and functionality while retaining the identical original amino acid sequence. Conclusion: Genetic codes control protein synthesis and folding. "Codon-preferred" DNA template(s) can be generated by functional screening. Significance: Protein properties can be considerably altered by synonymous codons without substituting amino acids.

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Section: Discussionmentioning

confidence: 99%

Genetic Code-guided Protein Synthesis and Folding in Escherichia coli

Wang

Cai

et al. 2013

Journal of Biological Chemistry

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“…In regard to tRNA modifications, their functions include: stability and flexibility of the tRNA structure (Motorin and Helm 2010), translational fidelity via codon-anticodon interaction (Saint-Léger and Ribas de Pouplana 2015), reading frame maintenance (Waas et al 2007;Delaunay et al 2016;Klassen et al 2016a), tRNA discrimination , nonsense suppression (Benko et al 2000), tRNA stability (Alexandrov et al 2006;Kotelawala et al 2008;Dewe et al 2012), proteome integrity (Nedialkova and Leidel 2015), sensitivity to aminoglycoside antibiotics acting at the decoding site of ribosomes (Kalhor and Clarke 2003), response to stress (Kamenski et al 2007;Chan et al 2012;Gu et al 2014), and recognition of tRNA as either self or nonself by TLR7 receptor (Kaiser et al 2014;Rimbach et al 2015). For general reviews, see Helm (2011), Hopper (2013) and Phizicky and Hopper (2015).…”

Section: The State Of the Trna Population In The Cellmentioning

confidence: 99%

Protein folding and tRNA biology

2017

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Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

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“…Oxidative or heat stress can result in changes in tRNA modification which, in turn, can result in translational reprogramming (Kamenski et al 2007;Chan et al 2012). Trm4 catalyzes m 5 C modification of tRNA Leu CAA at the wobble position 34 upon oxidative stress induced by hydrogen peroxide.…”

Section: Removal Of 59 Leader and 39 Trailer Sequences From Pre-trnasmentioning

confidence: 99%

“…Trm4 catalyzes m 5 C modification of tRNA Leu CAA at the wobble position 34 upon oxidative stress induced by hydrogen peroxide. m 5 C-modified tRNA Leu CAA results in increased translation of UUG, thereby increasing levels of at least one protein whose message is rich in UUG codons (Chan et al 2012). Loss of Trm4 results in sensitivity to paromomycin and oxidative stress (Wu et al 1998;Chan et al 2012).…”

Section: Removal Of 59 Leader and 39 Trailer Sequences From Pre-trnasmentioning

confidence: 99%

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

2013

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Transfer RNAs (tRNAs) are essential for protein synthesis. In eukaryotes, tRNA biosynthesis employs a specialized RNA polymerase that generates initial transcripts that must be subsequently altered via a multitude of post-transcriptional steps before the tRNAs beome mature molecules that function in protein synthesis. Genetic, genomic, biochemical, and cell biological approaches possible in the powerful Saccharomyces cerevisiae system have led to exciting advances in our understandings of tRNA post-transcriptional processing as well as to novel insights into tRNA turnover and tRNA subcellular dynamics. tRNA processing steps include removal of transcribed leader and trailer sequences, addition of CCA to the 39 mature sequence and, for tRNA His , addition of a 59 G. About 20% of yeast tRNAs are encoded by intron-containing genes. The three-step splicing process to remove the introns surprisingly occurs in the cytoplasm in yeast and each of the splicing enzymes appears to moonlight in functions in addition to tRNA splicing. There are 25 different nucleoside modifications that are added post-transcriptionally, creating tRNAs in which 15% of the residues are nucleosides other than A, G, U, or C. These modified nucleosides serve numerous important functions including tRNA discrimination, translation fidelity, and tRNA quality control. Mature tRNAs are very stable, but nevertheless yeast cells possess multiple pathways to degrade inappropriately processed or folded tRNAs. Mature tRNAs are also dynamic in cells, moving from the cytoplasm to the nucleus and back again to the cytoplasm; the mechanism and function of this retrograde process is poorly understood. Here, the state of knowledge for tRNA post-transcriptional processing, turnover, and subcellular dynamics is addressed, highlighting the questions that remain. TABLE OF CONTENTS Abstract 43Introduction 44

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

Cited by 379 publications

References 48 publications

Genetic Code-guided Protein Synthesis and Folding in Escherichia coli

Genetic Code-guided Protein Synthesis and Folding in Escherichia coli

Protein folding and tRNA biology

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

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