A shift in tRNA modifications and abundance during T-cell activation

The abundance of available transfer RNAs (tRNA) in a cell determines the efficiency, throughput, and accuracy of conversion of the protein-coding transcriptome into the proteome. We have previously identified a differential codon usage in proliferative cancerous cells and arrested/differentiated cells, which is coordinated with changes in the tRNA pool. Does normal programmed proliferation differs from cancerous proliferation? T-cells activation is a non-cancerous cell proliferation process, which is characterized by massive clonal expansion. We analyzed the transcriptome from naïve mice T-cells and during the activation process. We uncovered a striking difference in translation demand for certain codons. In parallel, we measured and analyzed tRNA expression changes in those cells using a tRNA deep sequencing approach. This method allows us to measure both the tRNA expression levels and certain post-transcriptional modification based on reverse transcription failures. We have found that changes in tRNA expression result in higher translation efficiency of the differentially expressed genes in the proliferative state. We further found that two types of tRNA modifications are reduced dramatically during T-cells activation. The two particular tRNA modifications, Wybutosine and ms26A, are known to encode highly slippery codons and to be involved in ribosome frameshift (FS) prevention. Governing the FS rate might play a role in HIV infection cycle due to programmed FS in the gag-pol protein. We used fluorescent FS reporter to validate the connection between the modification levels and FS rate. The changes in tRNA expression and modifications uncover a layer of translation regulation during the process of immune-cells clonal expansion.