Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest

Aharon-Heferz, Noa; Frumkin, Idan; Mayshar, Yoav; Dahan, Orna; Pilpel, Yitzhak; Rak, Roni

doi:10.1101/2020.04.30.070789

Cited by 4 publications

(6 citation statements)

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“…Induction of a Proliferation tRNA Signature Is Followed by Relaxation at the Differentiation Phase. We next set to examine what the changes are in the tRNA pool and if they correspond to the changes in demand as reflected by the codon usage, adapting a recently developed tRNA sequencing protocol (26) [see Materials and Methods for further details and Aharon-Hefetz et al (8) for additional quality assessment]. In the downstream analysis, we grouped together read counts of all tRNAs of the same anticodon that have at least a minimal tRNAScan prediction score [tRNAscan-SE (27)] above 50.…”

Section: Resultsmentioning

confidence: 99%

“…To determine which modifications can be detected using tRNA-seq we crossed annotated modification positions from the MODOMICS database (9), with tRNA-sequencing data collected in this study and human (8) and Escherichia coli (38) data from previous studies. We found that out of 46 modification types annotated in MODOMICS for the indicated species, 13 modifications were detected based on mismatches or RT abortions in our protocol (SI Appendix, Fig.…”

Section: ]) (E)mentioning

confidence: 99%

“…In particular, mRNAs (messenger RNAs) corresponding to cell-autonomous functions, related to proliferating cells, are enriched with a specific set of codons, while mRNA of multicellular functions, related to nondividing cells, are enriched with a different set of preferred codons. The tRNA pool in these cells is dynamically regulated and its dynamic corresponds to the changes in codon usage, as also reflected in differential tRNA essentiality in proliferation and cell arrest (7,8). Following these observations, it is essential to explore how the tRNA pool changes in a natural proliferation process, and what the contributions of the tRNA pool regulation to the integrity dynamics and of the immune response are.…”

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Dynamic changes in tRNA modifications and abundance during T cell activation

Rak

Polonsky

Eizenberg-Magar

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA (transfer RNA) supply and mRNA (messenger RNA) demand during cancerous proliferation. Yet dynamic changes may also occur during physiologically normal proliferation, and these are less well characterized. We examined the tRNA and mRNA pools of T cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observed a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool relaxed back to the basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T cell activation. These modifications occur in the anticodon loops of two tRNAs that decode “slippery codons,” which are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with an HIV gag-pol frameshifting site reporter. These results may explain HIV’s specific tropism toward proliferating T cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a layer of translation regulation during T cell proliferation and expose a potential tradeoff between cellular growth and translation fidelity.

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Section: Resultsmentioning

confidence: 99%

Section: ]) (E)mentioning

confidence: 99%

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Dynamic changes in tRNA modifications and abundance during T cell activation

Rak

Polonsky

Eizenberg-Magar

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…4 ) is further supported by data showing that the tRNA-ome expressed is reflective of the proliferative status of tissues [ 48 ]. Subsequent work has shown that by targeting individual tRNA families with the CRISPR-Cas9 system, most of the identified proliferation-promoting tRNAs were essential in rapidly dividing cells, with the tRNAs associated with differentiation showing higher essentiality in cells with a slower doubling time [ 96 ]. Although these differences could be assigned to the proliferative state of the cell, it seemed that the cellular origin was also an important factor [ 96 ].…”

Section: Mechanisms That Coordinate the Response To Codon Optimalitymentioning

confidence: 99%

Codon optimality in cancer

2021

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A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of ‘optimality’ for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.

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“…In particular, mRNAs corresponding to cell-autonomous functions, related to proliferating cells, are enriched with a specific set of codons, while mRNA of multicellular functions, related to non-dividing cells, are enriched with a different set of preferred codons. The tRNA pool in these cells is dynamically regulated and its dynamics corresponds to the changes in codon usage, as also reflected in differential tRNA essentiality in proliferation and cell arrest 7,8 . Following these observations, it is essential to explore how does the tRNA pool change in a natural proliferation process, and what are the contributions of the tRNA pool regulation to the integrity dynamics and of the immune response.…”

Section: Introductionmentioning

confidence: 99%

Dynamic changes in tRNA modifications and abundance during T-cell activation

Rak

Polonsky

Eizenberg

et al. 2020

Preprint

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The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of Tcells during their vigorous proliferation and differentiation upon triggering of the T cell antigen receptor. We observe a global signature of switch in demand for codon at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation of the T cells, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, Wybutosine and ms 2 t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode "slippery codons", that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a Wybutosine writer showed increased ribosomal frameshifting, as detected with a reporter that consists of a critical frameshifting site taken from the HIV gag-pol slippery codon motif. These results may explain HIV's specificity to proliferating T-Cells since it requires ribosomal frameshift exactly on this codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.The tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation-T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which relex when cells reduces their proliferation rate. We also found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication.

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Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest

Cited by 4 publications

References 57 publications

Dynamic changes in tRNA modifications and abundance during T cell activation

Dynamic changes in tRNA modifications and abundance during T cell activation

Codon optimality in cancer

Dynamic changes in tRNA modifications and abundance during T-cell activation

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