Skip to content
DraconiticResearch
Search Sources API
203,234 studies31 sourcesUpdated 53 min ago
Peer-reviewedCC BY-NC-NDNature Microbiology

Spatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria

  • Seunghyeon Kim1,2,3
  • Yan Zhang4,5
  • Xiangwu Ju6,7
  • Albur Hassan2
  • Yu-Huan Wang2
  • Shixin Liu6
  • Sangjin Kim1,2,3
7 affiliations
  1. 1Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA. [email protected]
  2. 2Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA
  3. 3Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA. [email protected]
  4. 4Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA. [email protected]
  5. 5Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA. [email protected]
  6. 6Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
  7. 7Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
Open at sourcePDFDOICite

Abstract

Bacterial gene expression is thought to involve tightly coupled transcription, translation and mRNA degradation. However, recent work has indicated that this is not always the case, leaving the generality and regulation of this coordination unclear. Here we use genetic, kinetic and spatial analyses in Escherichia coli to show that transcription–translation coupling requires high translational activity and that nearly half of the transcriptome exhibits signatures consistent with partial uncoupling. We find that co-transcriptional mRNA degradation is rare due to membrane localization of RNase E, except for transcripts encoding inner-membrane proteins. Our results show that translation efficiency determines the level of premature transcription termination, which in turn shapes mRNA degradation patterns and kinetics. Comparative analyses in Bacillus subtilis and Caulobacter crescentus also reveal species-specific coordination strategies. This challenges the universality of co-transcriptional coupling and defines how spatial and genetic features coordinate bacterial gene expression. RNase E localization and translation initiation coordinate transcription, translation and mRNA degradation during the life cycle of an mRNA, explaining gene- and species-specific variations in this coordination in bacteria.

Related

  1. Antiviral immunity via telomerase-like reverse transcription in bacteria
    Stephen Tang, Josephine L. Ramirez, Qixiang He +11
    NaturePeer-reviewedLicence not statedFull text9 citedEcologyMicrobiologyOpenAlex
  2. A transcription factor regulates development of a bacteria-housing eukaryotic cell through DNA damage mitigation
    Na-Na Li, Shan Jiang, Ji-Sheng Hong +5
    Proceedings of the National Academy of Sciences of the United States of AmericaPeer-reviewedCC BY-NC-ND 4.0Full textEcologyHAL
  3. Machine learning-assisted Repli-Histo labeling reveals distinct transcription-dependent constraints on chromatin motion in living cells
    Katsuhiko Minami, Kako Nakazato, Kai Shimizu +4
    Cell ReportsPeer-reviewedCC BY 4.0General biologyCrossref
  4. Bacteria sense virus-induced genome degradation via methylated mononucleotides
    Ilya А. Osterman, Bohdana Hurieva, Sarit Moses +6
    SciencePeer-reviewedCC BY5 citedEcologyMicrobiologyOpenAlex
  5. The core interaction network of transcription elongation factors is broadly maintained across diverse bacteria
    Thao N. P. Tran, Reid E. Peterson, Xiaofang Jiang +5
    mBioPeer-reviewedCC BY 4.0Full textGenetics & genomicsCrossref

Cite

BibTeXRIS
BibTeX
@article{kim2026spatial,
  title = {{Spatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria}},
  author = {Seunghyeon Kim and Yan Zhang and Xiangwu Ju and Albur Hassan and Yu-Huan Wang and Shixin Liu and Sangjin Kim},
  journal = {Nature Microbiology},
  year = {2026},
  month = may,
  doi = {10.1038/s41564-026-02374-8},
  url = {https://doi.org/10.1038/s41564-026-02374-8},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Spatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria
AU  - Seunghyeon Kim
AU  - Yan Zhang
AU  - Xiangwu Ju
AU  - Albur Hassan
AU  - Yu-Huan Wang
AU  - Shixin Liu
AU  - Sangjin Kim
PY  - 2026
DA  - 2026/05/22
JO  - Nature Microbiology
DO  - 10.1038/s41564-026-02374-8
UR  - https://doi.org/10.1038/s41564-026-02374-8
AB  - Bacterial gene expression is thought to involve tightly coupled transcription, translation and mRNA degradation. However, recent work has indicated that this is not always the case, leaving the generality and regulation of this coordination unclear. Here we use genetic, kinetic and spatial analyses in Escherichia coli to show that transcription–translation coupling requires high translational activity and that nearly half of the transcriptome exhibits signatures consistent with partial uncoupling. We find that co-transcriptional mRNA degradation is rare due to membrane localization of RNase E, except for transcripts encoding inner-membrane proteins. Our results show that translation efficiency determines the level of premature transcription termination, which in turn shapes mRNA degradation patterns and kinetics. Comparative analyses in Bacillus subtilis and Caulobacter crescentus also reveal species-specific coordination strategies. This challenges the universality of co-transcriptional coupling and defines how spatial and genetic features coordinate bacterial gene expression. RNase E localization and translation initiation coordinate transcription, translation and mRNA degradation during the life cycle of an mRNA, explaining gene- and species-specific variations in this coordination in bacteria.
SN  - 2058-5276
ER  -