Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.

The expanding world of tRNA modifications and their disease relevance

Abstract Aggressive and metastatic cancers show enhanced metabolic plasticity 1 , but the precise underlying mechanisms of this remain unclear. Here we show how two NOP2/Sun RNA methyltransferase 3 (NSUN3)-dependent RNA modifications—5-methylcytosine (m 5 C) and its derivative 5-formylcytosine (f 5 C) (refs. 2–4 )—drive the translation of mitochondrial mRNA to power metastasis. Translation of mitochondrially encoded subunits of the oxidative phosphorylation complex depends on the formation of m 5 C at position 34 in mitochondrial tRNA Met . m 5 C-deficient human oral cancer cells exhibit increased levels of glycolysis and changes in their mitochondrial function that do not affect cell viability or primary tumour growth in vivo; however, metabolic plasticity is severely impaired as mitochondrial m 5 C-deficient tumours do not metastasize efficiently. We discovered that CD36-dependent non-dividing, metastasis-initiating tumour cells require mitochondrial m 5 C to activate invasion and dissemination. Moreover, a mitochondria-driven gene signature in patients with head and neck cancer is predictive for metastasis and disease progression. Finally, we confirm that this metabolic switch that allows the metastasis of tumour cells can be pharmacologically targeted through the inhibition of mitochondrial mRNA translation in vivo. Together, our results reveal that site-specific mitochondrial RNA modifications could be therapeutic targets to combat metastasis. 

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Mitochondrial RNA modifications shape metabolic plasticity in metastasis

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Transfer RNA (tRNA) molecules are posttranscriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as "tRNA modopathies". Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.

Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications.

Abstract RNA modifications are important regulatory elements of RNA functions. However, most genome-wide mapping of RNA modifications has focused on messenger RNAs and transfer RNAs, but such datasets have been lacking for small RNAs. Here we mapped N 1 -methyladenosine (m 1 A) in the cellular small RNA space. Benchmarked with synthetic m 1 A RNAs, our workflow identified specific groups of m 1 A-containing small RNAs, which are otherwise disproportionally under-represented. In particular, 22-nucleotides long 3′ tRNA-fragments are highly enriched for TRMT6/61A-dependent m 1 A located within the seed region. TRMT6/61A-dependent m 1 A negatively affects gene silencing by tRF-3s. In urothelial carcinoma of the bladder, where TRMT6/61A is over-expressed, higher m 1 A modification on tRFs is detected, correlated with a dysregulation of tRF targetome. Lastly, TRMT6/61A regulates tRF-3 targets involved in unfolded protein response. Together, our results reveal a mechanism of regulating gene expression via base modification of small RNA. 

/pdf/trmt6-61a-dependent-base-methylation-of-trna-derived-1t4yxxb2.pdf

TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer

Mitochondria generate most cellular energy via oxidative phosphorylation. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA translate essential subunits of the respiratory chain complexes. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. They are required for deciphering genetic code accurately, as well as stabilizing tRNA. Loss of tRNA modifications frequently results in severe pathological consequences. Here, we perform a comprehensive analysis of post-transcriptional modifications of all human mt-tRNAs, including 14 previously-uncharacterized species. In total, we find 18 kinds of RNA modifications at 137 positions (8.7% in 1575 nucleobases) in 22 species of human mt-tRNAs. An up-to-date list of 34 genes responsible for mt-tRNA modifications are provided. We identify two genes required for queuosine (Q) formation in mt-tRNAs. Our results provide insight into the molecular mechanisms underlying the decoding system and could help to elucidate the molecular pathogenesis of human mitochondrial diseases caused by aberrant tRNA modifications. Mitochondrial tRNA modifications are important for tRNA stability and accurate decoding. By employing RNA mass spectrometry and deep sequencing, here the authors provide a comprehensive analysis of post-transcriptional modifications of 22 species of human mitochondrial tRNAs.

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Complete chemical structures of human mitochondrial tRNAs

Hydrogen storage by means of catalytic hydrogenation of suitable organic substrates helps to elevate the volumetric density of hydrogen energy. In this regard, utilizing cheaper industrial crude hydrogen to fulfill the goal of hydrogen storage would show economic attraction. However, because CO impurities in crude hydrogen can easily deactivate metal active sites even in trace amounts such a process has not yet been realized. Here, we develop a robust RuNi/TiO2 catalyst that enables the efficient hydrogenation of toluene to methyl-cyclohexane under simulated crude hydrogen feeds with 1000-5000 ppm CO impurity at around 180 °C under atmospheric pressure. We show that the co-localization of Ru and Ni species during reduction facilitated the formation of tightly coupled metallic Ru-Ni clusters. During the catalytic hydrogenation process, due to the distinct bonding properties, Ru and Ni served as the active sites for CO methanation and toluene hydrogenation respectively. Our work provides fresh insight into the effective utilization and purification of crude hydrogen for the future hydrogen economy. 

/pdf/co-tolerant-runi-tio-2-catalyst-for-the-storage-and-1pimae8i.pdf

CO-tolerant RuNi/TiO_2 catalyst for the storage and purification of crude hydrogen

https://doi.org/10.1016/j.xinn.2022.100353

Direct utilization of crude and waste H2 via CO-tolerant hydrogenation

In the March issue of <i>Chem</i>, Jung and co-workers demonstrated a universal route for identifying the quantitative contribution of active sites in supported catalysts. Combining electronic tomography, catalytic evaluation, and density functional theory (DFT) calculations, the authors provide an analytic approach to correlating reaction pathways with specific active sites for various reactions. 

Ding Ma

Papers

Complete chemical structures of human mitochondrial tRNAs

CO-tolerant RuNi/TiO_2 catalyst for the storage and purification of crude hydrogen

Direct utilization of crude and waste H2 via CO-tolerant hydrogenation

Envisioning quantitative catalytic superiority of interfacial sites in three dimensions