Perturbation of apoptosis upon binding of tRNA to the heme domain of cytochrome c

Oxidative Modifications of RNA and Its Potential Roles in Biosystem

Elevated level of oxidized RNA was detected in vulnerable neurons in Alzheimer patients. Subsequently, several diseases and pathological conditions were reported to be associated with RNA oxidation. In addition to several oxidized derivatives, cross-linking and unique strand breaks are generated by RNA oxidation. With a premise that dysfunctional RNA mediated by oxidation is the pathogenetic molecular mechanism, intensive investigations have revealed the mechanism for translation errors, including premature termination, which gives rise to aberrant polypeptides. To this end, we and others revealed that mRNA oxidation could compromise its translational activity and fidelity. Under certain conditions, oxidized RNA can also induce several signaling pathways, to mediate inflammatory response and induce apoptosis. In this review, we focus on the oxidative modification of RNA and its resulting effect on protein synthesis as well as cell signaling. In addition, we will also discuss the potential roles of enzymatic oxidative modification of RNA in mediating cellular effects.

Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology

Transfer tRNAs (tRNAs) are small non-coding RNAs that are highly conserved in all kingdoms of life. Originally discovered as the molecules that deliver amino acids to the growing polypeptide chain during protein synthesis, tRNAs have been believed for a long time to play exclusive role in translation. However, recent studies have identified key roles for tRNAs and tRNA-derived small RNAs in multiple other processes, including regulation of transcription and translation, posttranslational modifications, stress response, and disease. These emerging roles suggest that tRNAs may be central players in the complex machinery of biological regulatory pathways. Here we overview these non-canonical roles of tRNA in normal physiology and disease, focusing largely on eukaryotic and mammalian systems.

Noncanonical inputs and outputs of tRNA aminoacylation

The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.

tRNA Deregulation and Its Consequences in Cancer

The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.

Cytochrome c Catalyzes the Hydrogen Peroxide-Assisted Oxidative Desulfuration of 2-Thiouridines in Transfer RNAs

The 5-substituted 2-thiouridines (R5S2Us) present in the first (wobble) position of the anticodon of transfer RNAs (tRNAs) contribute to accuracy in reading mRNA codons and tuning protein synthesis. Previously, we showed that, under oxidative stress conditions in vitro, R5S2Us were sensitive to hydrogen peroxide (H₂ O₂ ) and that their oxidative desulfuration produced 5-substituted uridines (R5Us) and 4-pyrimidinone nucleosides (R5H2Us) at a ratio that depended on the pH and an R5 substituent. Here, we demonstrate that the desulfuration of 2-thiouridines, either alone or within an RNA/tRNA chain, is catalyzed by cytochrome c (cyt c). Its kinetics are similar to those of Fenton-type catalytic 2-thiouridine (S2U) desulfuration. Cyt c/H₂ O₂ - and Fe^II -mediated reactions deliver predominantly 4-pyrimidinone nucleoside (H2U)-type products. The pathway of the cyt c/H₂ O₂ -peroxidase-mediated S2U→H2U transformation through uridine sulfenic (U-SOH), sulfinic (U-SO₂ H), and sulfonic (U-SO₃ H) intermediates is confirmed by LC-MS. The cyt c/H₂ O₂ -mediated oxidative damage of S2U-tRNA may have biological relevance through alteration of the cellular functions of transfer RNA.

Elucidation of tRNA-cytochrome c interactions through hydrogen/deuterium exchange mass spectrometry

Cytochrome c (cyt c) is a mitochondrial protein responsible for transferring electrons between electron transport chain complexes III and IV. The release of cyt c from the mitochondria has been considered as a commitment step in intrinsic apoptosis. Transfer RNA (tRNA) has recently been found to interact with the released cyt c to prevent the formation of the apoptosome complex, thus preventing cell apoptosis. To understand the molecular basis of tRNA-cyt c interactions, we applied hydrogen/deuterium exchange mass spectrometry (HDXMS) to analyze the interactions between tRNA and cyt c. tRNA^Phe binding to cyt c reduced the deuteration level of cyt c in all analyzed regions, indicating that tRNA binding blocks the solvent-accessible regions and results in the formation of a more compact conformation. Substitution of the tRNA^Phe with the total tRNA from brewer's yeast in the HDXMS experiment significantly reduced deuteration in the N-terminus and the region 18-32 residue of cyt c, where all tRNAs are bound. To clarify the cause of binding, we used synthesized single-stranded oligonucleotides of 12-mer dA and dT to form complexes with cyt c. The exchange of the nucleotide bases between adenine and thymine did not affect the deuteration level of cyt c. However, the regions 1-10 and 65-82 showed minor decreases after unstructured dA or dT DNA binding. Collectively, these results reveal that cyt c maintains its globular structure to interact with tRNA. The region 18-32 selectively interacts with tRNA, and N-terminal 1-10 interacts with oligonucleotides electrostatically.

Human mitochondrial MIA40 (CHCHD4) is a component of the Fe-S cluster export machinery

Mitochondria play an essential role in synthesis and export of iron-sulfur (Fe-S) clusters to other sections of a cell. Although the mechanism of Fe-S cluster synthesis is well elucidated, information on the identity of the proteins involved in the export pathway is limited. The present study identifies hMIA40 (human mitochondrial intermembrane space import and assembly protein 40), also known as CHCHD4 (coiled-coil-helix-coiled-coil-helix domain-containing 4), as a component of the mitochondrial Fe-S cluster export machinery. hMIA40 is an iron-binding protein with the ability to bind iron in vivo and in vitro. hMIA40 harbours CPC (Cys-Pro-Cys) motif-dependent Fe-S clusters that are sensitive to oxidation. Depletion of hMIA40 results in accumulation of iron in mitochondria concomitant with decreases in the activity and stability of Fe-S-containing cytosolic enzymes. Intriguingly, overexpression of either the mitochondrial export component or cytosolic the Fe-S cluster assembly component does not have any effect on the phenotype of hMIA40-depleted cells. Taken together, our results demonstrate an indispensable role for hMIA40 for the export of Fe-S clusters from mitochondria.

tRNAs as regulators of biological processes

Transfer RNAs (tRNA) are best known for their role as adaptors during translation of the genetic code. Beyond their canonical role during protein biosynthesis, tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression. Aminoacylated tRNAs have also been implicated as substrates for non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosyntheses. Most recently tRNA fragments, or tRFs, have also been recognized to play regulatory roles. Here, we examine in more detail some of the new functions emerging for tRNA in a variety of cellular processes outside of protein synthesis.

Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress

Adaptation to changes in extracellular tonicity is essential for cell survival. However, severe or chronic hyperosmotic stress induces apoptosis, which involves cytochrome c (Cyt c) release from mitochondria and subsequent apoptosome formation. Here, we show that angiogenin-induced accumulation of tRNA halves (or tiRNAs) is accompanied by increased survival in hyperosmotically stressed mouse embryonic fibroblasts. Treatment of cells with angiogenin inhibits stress-induced formation of the apoptosome and increases the interaction of small RNAs with released Cyt c in a ribonucleoprotein (Cyt c-RNP) complex. Next-generation sequencing of RNA isolated from the Cyt c-RNP complex reveals that 20 tiRNAs are highly enriched in the Cyt c-RNP complex. Preferred components of this complex are 5' and 3' tiRNAs of specific isodecoders within a family of isoacceptors. We also demonstrate that Cyt c binds tiRNAs in vitro, and the pool of Cyt c-interacting RNAs binds tighter than individual tiRNAs. Finally, we show that angiogenin treatment of primary cortical neurons exposed to hyperosmotic stress also decreases apoptosis. Our findings reveal a connection between angiogenin-generated tiRNAs and cell survival in response to hyperosmotic stress and suggest a novel cellular complex involving Cyt c and tiRNAs that inhibits apoptosome formation and activity.