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

Abstract

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.

Keywords: RNA-mediated signaling; arginylation; posttranslational modifications; tRNA; tsRNA.

FIGURE 1

tRNA maturation and structure. (A) Maturation of tRNA involves 5′ and 3′ processing, intron splicing, modification of nucleotides, and addition of 3′ CCA end. Mature tRNAs are charged with cognate amino acids by aminoacyl-tRNA synthetases (aaRSs). This reaction involves conjugation of cognate amino acid to the 3′ terminal adenosine of tRNA by an ester bond (Berg and Offengand, 1958). (B) The generic secondary structure of tRNA with its constituent domains marked in different colors: acceptor stem (red); dihydrouridine (D-) stem and loop (blue); anticodon stem and loop (green); variable (V-) loop (gray); and TΨC (T-) stem and loop (yellow). Anticodon sequence is depicted in darker blue-green within the anticodon loop and is numbered (nt 34–36). Discriminator base (N73) aiding in aaRS recognition is located upstream of the 3′CCA tail (Giege, 2008). (C) Schematic representation of the L-shaped tertiary structure of yeast tRNA^Phe. Loops are color-coded similarly to those in panel (B). The structure was derived from reported crystal structure (Protein Data Bank code 1EHZ) (Shi and Moore, 2000).

FIGURE 2

tRNA functions in various pathways in cell physiology. (1) Upon nutrient deficiency, binding of deacylated tRNAs to GCN2 leads to conformational changes of the kinase GCN2, resulting in phosphorylation of eIF2α. This causes repression of global protein synthesis, along with translation of activating transcription factor 4 (ATF4) in mammals and general control protein (GCN4) in yeast. These proteins induce selective expression of amino acid biosynthesis genes upon stress (Hinnebusch et al., 2016; Young and Wek, 2016). (2) Stress conditions trigger the release of cytochrome c (Cyt c) from mitochondria to the cytoplasm. In the cytoplasm, binding of tRNAs to Cyt c prevents association of Cyt c with Apaf-1. Thereby, the caspase cascade required for apoptosis is precluded (Mei et al., 2010; Suryanarayana et al., 2012; Gorla and Sepuri, 2014; Liu et al., 2016). (3) Aminoacyl-tRNAs serve as a donors in posttranslational modifications. (4) In protein arginylation, ATE1 transfers Arg from arginyl-tRNA^Arg onto a protein substrate. (5) tRNA is used as a primer in the reverse transcription of LTR retrotransposons (Martinez, 2017). (6) Dysregulation of individual tRNA contributes to the onset and severity of different diseases by impacting cellular programs. (7) Mismethylation of tRNAs is induced in response to stress conditions. Extra incorporation of Met in newly synthesized proteins serves an evolutionary strategy for expanding the genetic information in proteins (Netzer et al., 2009; Wiltrout et al., 2012; Lee et al., 2014; Wang and Pan, 2015; Schwartz et al., 2016). (8) Generation of tRNA-derived small RNAs leads to global regulatory responses (Keam and Hutvagner, 2015; Xie et al., 2020).

FIGURE 3

tRNAs play a protective role in the intrinsic apoptosis pathway. An internal stimulus, e.g., DNA damage or viral infection, causes the loss of mitochondrial membrane potential and leads to a release of cytochrome c (Cyt c) to the cytoplasm. Cytosolic Cyt c binds to the death adaptor apoptotic protease-activating factor-1 (Apaf-1) and ATP, triggering assembly of the oligomeric apoptosome complex, which recruits procaspase-9, leading to its activation. Caspase-9 activates effector caspases, e.g., caspase-3/7, and eventually leads to cell death. In this pathway, tRNAs directly bind to Cyt c and prevent Cyt c association with Apaf-1 and apoptosis.

FIGURE 4

Biogenesis and classification tsRNAs. tsRNAs are divided into two main types, tiRNA (red) and tRF (blue). tiRNAs are produced by a specific cleavage at the anticodon loop of mature tRNA, generating two fragments, 5′-tiRNA and 3′-tiRNA. This cleavage is mediated by angiogenin (ANG), mostly under stress conditions. 5- and 3-tRF are produced by a specific cleavage at or near D- and T-loops of mature tRNAs. “a,” “b,” and “c” for 5-tRFs and 3-tRFs to define fragments of different length (∼15–18, 22, and 31 nt, respectively). The enzymes mediating this cleavage are not fully characterized but are believed to involve endonuclease Dicer and/or RNase T2. 2-tRF is derived from the internal region and generated by the unknown cleavage method. 1-tRF contains 3′-trailer, produced by RNase Z/ELAC2. tsRNA, tRNA-derived small RNA, tiRNA, stress induced tRNA fragment, tRF, tRNA-derived fragment.

FIGURE 5

tsRNAs play regulatory functions in cell physiology. Examples of tsRNA functions include inhibition of translation initiation, repression of global protein synthesis, translational repression and mRNA cleavage, regulation of retrotransposition, and utilization of protein arginylation.