Journal article
Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs
mBio, Vol.16(7), e00875-25
07/09/2025
DOI: 10.1128/mbio.00875-25
PMCID: PMC12239594
PMID: 40444975
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports the biological function for tRNA cleavage products, including the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus 68, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by ordered two template relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, which regulates tRNA splicing among other RNA processing events, is required for efficient MHV68 replication. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.IMPORTANCEDiverse conditions of infection and cellular stress incite the cleavage of transfer RNAs (tRNAs), leading to the formation of tRNA fragments (tRFs) that can directly regulate gene expression. In our study of gammaherpesviruses, such as murine herpesvirus 68 and human oncogenic Kaposi sarcoma-associated herpesvirus, we discovered that tRNA regulation and cleavage are key components of gene reprogramming during infection. We present the first in-depth profile of tRF generation in response to DNA virus infection, using state-of-the-art sequencing techniques that overcome several challenges with tRNA sequencing. We present several lines of evidence that tRFs are made from newly transcribed premature tRNAs and propose that this may be a defining characteristic of tRNA cleavage during infection. Finally, we show that tRNA splicing machinery is involved with the formation of some MHV68-induced tRFs, with a key regulator of splicing, CLP1, required for maximal viral titer. Taken together, we posit that tRNA processing may be integral to the elegant shift in gene expression that occurs during viral takeover of the host cell.
Details
- Title: Subtitle
- Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs
- Creators
- Aidan C Manning - University of California, Santa CruzMahmoud M Bashir - University of IowaKyle Rapchak - University of Iowa, Microbiology and ImmunologyCalyssa J Huff - Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USAAriana R Jimenez - University of IowaSheila Gonzalez - University of IowaCourtney L Woodruff - University of IowaHeather E Upton - University of California, BerkeleyKathleen Collins - University of California, BerkeleyTodd M Lowe - University of California, Santa CruzJessica M Tucker - University of Iowa
- Resource Type
- Journal article
- Publication Details
- mBio, Vol.16(7), e00875-25
- DOI
- 10.1128/mbio.00875-25
- PMID
- 40444975
- PMCID
- PMC12239594
- NLM abbreviation
- mBio
- ISSN
- 2150-7511
- eISSN
- 2150-7511
- Publisher
- American Society for Microbiology
- Grant note
- American Cancer Society
The authors thank Lucas Ferguson for his contributions to the development and optimization of OTTR, as well as all present and past members of the Tucker, Lowe, Glaunsinger, and Roller labs for their helpful suggestions, discussion, and careful reading of the manuscript.
- Language
- English
- Electronic publication date
- 05/30/2025
- Date published
- 07/09/2025
- Academic Unit
- Microbiology and Immunology
- Record Identifier
- 9984824169902771
Metrics
6 Record Views