Tie-Break: Host and Retrotransposons Play tRNA

Abstract

tRNA fragments (tRFs) are a class of small, regulatory RNAs with diverse functions. 3'-Derived tRFs perfectly match long terminal repeat (LTR)-retroelements which use the 3'-end of tRNAs to prime reverse transcription. Recent work has shown that tRFs target LTR-retroviruses and -transposons for the RNA interference (RNAi) pathway and also inhibit mobility by blocking reverse transcription. The highly conserved tRNA primer binding site (PBS) in LTR-retroelements is a unique target for 3'-tRFs to recognize and block abundant but diverse LTR-retrotransposons that become transcriptionally active during epigenetic reprogramming in development and disease. 3'-tRFs are processed from full-length tRNAs under so far unknown conditions and potentially protect many cell types. tRFs appear to be an ancient link between RNAi, transposons, and genome stability.

Keywords: LTR-retrotransposon; primer binding site; retrovirus; small RNA; tRF; tRNA.

Figure 1.. Reverse Transcription of LTR-Retrotransposons and -Viruses.

Long terminal repeats (LTR) encode promoter elements and termination signals. The RNA transcript contains a region repeated at either end (R), a segment unique to the 5’ end of the RNA (U5), and a segment only included at the 3’-end of the RNA (U3). The 3’-end of cellular tRNAs (red cloverleaf) primes reverse transcription by hybridizing to the primer binding site (PBS). While this segment is being copied into first-strand cDNA (brown line), also called (−)ssDNA (minus strong stop DNA), the RNaseH activity of RT degrades the template RNA. The elongating cDNA is transferred to the 3’-end of the retrotransposon transcript by hybridizing to the R region. The remaining RNA is partially degraded by RNaseH leaving behind primers for second-strand cDNA synthesis. After another transfer event, first- and second-strand synthesis are completed to result in a full-length, double-stranded retroviral DNA that will be integrated into the host genome.

Figure 2.. Model of LTR-Retroelement Silencing by 3’-tRFs.

LTR-retroelements comprise LTR-retrotransposons and LTR-retroviruses. In the absence of epigenetic suppression, non-coding and coding LTR-retroelements are transcribed. Elements that encode the enzymatic machinery for retroviral replication are autonomous and in the first step their RNA is spliced and translated. 22 nt 3’-tRFs (tRF3-b) target coding-competent LTR-retroelements at the level of retroviral protein production through post-transcriptional gene silencing. Retroviral gene products of the autonomous, coding element constitute all components of the retroviral particle and recruit virus “genomic” unspliced RNA template of both coding and non-coding family members as well as host-dependent co-factors like tRNAs to the particle. 18 nt 3’-tRFs (tRF3-a) interfere with reverse transcription at the level of first-strand synthesis and therefore inhibit both coding and noncoding, non-autonomous retrotransposons. 3’-tRFs specifically promote silencing of any potentially mobile LTR-retroelement that has maintained a functional PBS. PBS, primer binding site; RT, reverse transcriptase.

Figure 3.. tRNA Structure and Domains

Three alternative representations of the same tRNA, here of tRNA Lys-AAA with the anticodon-sequence UUU, illustrate its functional domains and tertiary structure. (A) The typical cloverleaf diagram provides an overview of the major domains and loops. The acceptor stem has the post-transcriptional CCA-tag at its 3’-end that will be covalently linked with the amino-acid prior to translation. (B) The three-dimensional L-shaped structure of tRNA is composed of two double-stranded helices: (C) the anticodon-D-loop (black/grey) that serves proof-reading functions during translation at the ribosome and the upper minihelix (green) consisting of the acceptor-stem and the TψC-loop. (Figure modified from [58]).