A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation

PLoS Pathog. 2022 Sep 15;18(9):e1010827. doi: 10.1371/journal.ppat.1010827. eCollection 2022 Sep.

Abstract

RNA-sequencing has led to a spectacular increase in the repertoire of bacterial sRNAs and improved our understanding of their biological functions. Bacterial sRNAs have also been found in outer membrane vesicles (OMVs), raising questions about their potential involvement in bacteria-host relationship, but few studies have documented this issue. Recent RNA-Sequencing analyses of bacterial RNA unveiled the existence of abundant very small RNAs (vsRNAs) shorter than 16 nt. These especially include tRNA fragments (tRFs) that are selectively loaded in OMVs and are predicted to target host mRNAs. Here, in Escherichia coli (E. coli), we report the existence of an abundant vsRNA, Ile-tRF-5X, which is selectively modulated by environmental stress, while remaining unaffected by inhibition of transcription or translation. Ile-tRF-5X is released through OMVs and can be transferred to human HCT116 cells, where it promoted MAP3K4 expression. Our findings provide a novel perspective and paradigm on the existing symbiosis between bacteria and human cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Proliferation
  • Escherichia coli* / genetics
  • Gene Expression
  • Humans
  • RNA, Bacterial* / genetics
  • RNA, Transfer / genetics

Substances

  • RNA, Bacterial
  • RNA, Transfer

Grants and funding

This work, and the article processing charge (APC) were funded by Natural Sciences and Engineering Research Council of Canada (NSERC; https://www.nserc-crsng.gc.ca) Discovery Grant number RGPIN-2019-06502 (to P.P.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.