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Peer-reviewedCC BY 4.0mBio

Growth-dependent tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis

  • Michelle M. Mitchener1
  • Caleb M. Anderson2
  • Mark Veleba3
  • Kayla Teo1
  • Mélanie Roch2
  • Ruixi Chen4
  • Yifeng Yuan4
  • Isaiah Han1
  • Agnieszka Dziergowska5
  • Kevin Pethe1,3,6,7
  • Thomas J. Begley8,9
  • Kimberly A. Kline1,2,3,10
1 more authors
  • Peter C. Dedon1,4
10 affiliations
  1. 1Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore
  2. 2Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
  3. 3Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
  4. 4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
  5. 5Institute of Organic Chemistry, Lodz University of Technology, Lodz, Poland
  6. 6Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
  7. 7National Centre for Infectious Diseases (NCID), Singapore, Singapore
  8. 8Department of Biological Sciences, University at Albany, Albany, New York, USA
  9. 9RNA Institute, University at Albany, Albany, New York, USA
  10. 10School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Abstract

Enterococcus faecalis is a gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis, how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem-loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.

IMPORTANCE: Enterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism’s physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for posttranscriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.

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Cite

BibTeXRIS
BibTeX
@article{mitchener2026growthdependent,
  title = {{Growth-dependent tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis}},
  author = {Michelle M. Mitchener and Caleb M. Anderson and Mark Veleba and Kayla Teo and Mélanie Roch and Ruixi Chen and Yifeng Yuan and Isaiah Han and Agnieszka Dziergowska and Kevin Pethe and Thomas J. Begley and Kimberly A. Kline and Peter C. Dedon},
  journal = {mBio},
  year = {2026},
  month = aug,
  doi = {10.1128/mbio.01474-26},
  url = {https://doi.org/10.1128/mbio.01474-26},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Growth-dependent tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis
AU  - Michelle M. Mitchener
AU  - Caleb M. Anderson
AU  - Mark Veleba
AU  - Kayla Teo
AU  - Mélanie Roch
AU  - Ruixi Chen
AU  - Yifeng Yuan
AU  - Isaiah Han
AU  - Agnieszka Dziergowska
AU  - Kevin Pethe
AU  - Thomas J. Begley
AU  - Kimberly A. Kline
AU  - Peter C. Dedon
PY  - 2026
DA  - 2026/08/31
JO  - mBio
DO  - 10.1128/mbio.01474-26
UR  - https://doi.org/10.1128/mbio.01474-26
AB  - Enterococcus faecalis is a gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis, how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem-loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.  IMPORTANCE: Enterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism’s physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for posttranscriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.
SN  - 2150-7511
ER  -