Nutritional control of protein translation and brain function via tRNA modification

Project number
01

Application deadline
17 Jan 2023 until 15 Mar 2023

Start of PhD
1 Feb 2023

Project leader 
Prof. Dr. Dr. Georg Stoecklin

Co project leader

Project title

Stoecklin_Tuorto - Nutritional control of protein translation and brain function via tRNA modification

Summary

Post-transcriptional modifications in the anticodon loop of tRNAs are important regulators of the decoding process during protein synthesis. We recently showed that nutritional determined levels of queuosine (Q), a bacteria-derived nucleoside found in eukaryotic tRNA, influence the levels of 5-methylcytosine (5mC) of C38-tRNA-Asp in human cell culture and in germ-free mice. Using proteomic and Ribo-Seq approaches, we discovered a direct connection between these anticodon loop tRNA modifications and the speed of codon-biased translation. Q-dependent translation at the level of single codons, especially at Q-decoded and near cognate-codons, promotes protein folding and prevents the accumulation of misfolded proteins.
Q-modifications of tRNA are conducted by tRNA-guaninetransglycosylase (TGT) composed of the QTRT1-QTRT2 enzyme complex.

The aim of the new project is to study how altered translation decoding affects brain functions. We will use two already established TGT knockout mouse models to study brain defects in vivo. The project will study if lack of Q modifications alters neurogenesis or alternatively induces neurodegeneration. The PhD student will use primary cultures of mouse hippocampal neurons, reporters of stalled ribosomes and inhibitors of protein translation regulators to further investigate if Q-tRNA affects processes like ribosome quality control (RQC), No-Go Decay (NGD) and eIF2 signaling. In parallel, using C. elegans as model system, she/he will determine if lack of Q-tRNA alters co-translational protein folding. Taken together, this project will analyse potential direct links between the altered decoding of the neuronal transcriptome by a bacterial micronutrient and the onset of neuronal phenotypes.

The project can start immediately; however, we are flexible with the starting time.

Reference

• Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA. Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. EMBO J. 2021 Mar 15;40(6):e105496.
• Legrand C, Tuorto F. RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data. Nucleic Acids Research. 2020 Jan 24;48(2):e7.
• Tuorto F, Legrand C, Cirzi C, Federico G, Liebers R, Müller M, Ehrenhofer-Murray AE, Dittmar G, Gröne HJ, Lyko F. (2018). Queuosine-modified tRNAs confer nutritional control of protein translation. EMBO J. e99777.
• Legrand C, Tuorto F, Hartmann M, Liebers R, Jacob D, Helm M, Lyko F. (2017). Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs. Genome Res. 27: 1589-1596.
• Tuorto F, Herbst F, Alerasool N, Bender S, Popp O, Federico G, Reitter S, Liebers R, Stoecklin G, Gröne HJ, Dittmar G, Glimm H, Lyko F. (2015). The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. EMBO J 34:2350-2362.
• Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F. (2012). RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol. 19:900-5.

Methods that will be used

Primary neuronal cell culture, histology and immunofluorescence, next generation RNA-sequencing, RNA modification analysis, Polysome profiling, Ribosome profiling, C. elegans and mouse in vivo model.

Cooperation partners

The project benefits from various established collaborations with neurobiologist and C elegans groups. Strong interactions are also entrenched in Mannheim/Heidelberg campus.

Personal qualifications

MSc in biology or related subjects; dedicated interest in RNA biology and neurobiology; strong background in cell biology, molecular biology. High motivation. Willing to work with animal models. Knowledge in bioinformatics will be a surplus.

Keywords

tRNA modifications, protein translation, neurobiology.