Translational response to mitochondrial stresses is orchestrated by tRNA modifications

Abstract

Mitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.

tRNA modifications inform tissue specific mRNA translation and codon optimization

“…In our work, we identified queuosine (tRNA-Q) to be preferentially enriched in the brain and drive NAY codon recognition. Queuosine modifications were shown to play important role in regulating cellular response to arsenite induced oxidative stress and mitochondrial stress and dysfunction (15,23), as well as playing a role in hippocampal neurons function and cognition (17). Interestingly, despite the reported importance of queuosine in codon decoding in vitro (18,23), Knockout mice were phenotypically normal apart from cognitive and memory dysfunction (17).…”

“…Queuosine modifications were shown to play important role in regulating cellular response to arsenite induced oxidative stress and mitochondrial stress and dysfunction (15,23), as well as playing a role in hippocampal neurons function and cognition (17). Interestingly, despite the reported importance of queuosine in codon decoding in vitro (18,23), Knockout mice were phenotypically normal apart from cognitive and memory dysfunction (17). In addition, such distinct phenotype indicates the importance of tRNA-Q in brain function, in line with previous works that showed that Queuine, the precursor for queuosine, is protective against neurodegenerative diseases (38) and our observation of queuosine enrichment in the brain.…”

“…tRNA modifications are known to drive mRNA translation by altering codon recognition, usage, and optimality (4,17,23,25). To elucidate the potential for such regulatory fine-tuning on tissue specific mRNA translation, we analyzed three metrics for codon analysis; isoacceptors codon frequency (which measures the enrichment of synonymous codons compared to each other), total codon frequency (which compares the expression of a codon with all other codons in the mRNA sequence) (34,35), and A-site pausing (which measures ribosome dwelling at each codon) (36) [Supplementary figure 7].…”

“…Previous works have elucidated the dynamic nature of tRNA epitranscriptome in regulating processes such as the stress response (6,15,(20)(21)(22)(23) and growth conditions (24) and how these dynamic changes impact codon recognition (6,23,25). Nonetheless, much remains to be elucidated on the role of tRNA epitranscriptome in regulating physiologic mRNA translation in various tissues and cells, and their role in tissue physiology.…”

Deciphering the Diversity in Bacterial Transporters That Salvage Queuosine Precursors

“…Recent studies have reinforced the importance of Q as a micronutrient [ 10 , 11 ], particularly for optimal brain function [ 12 , 13 ] and mitochondrial stress responses [ 14 ]. However, how the human host competes with organisms of the microbiome for Q precursors is poorly understood.…”