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PreprintCited by 1RNA and protein synthesis mechanismsBacterial Genetics and BiotechnologyBiochemical and Molecular Research

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Mechanistic insights into E. coli recovery from growth arrest

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Hassan, Ahmed, Nakano, Yuko, Gamper, Howard, Masuda, Isao, Pinkas, Matyas, Nagarajan, Sathya, Dworkin, Jonathan, Blaha, Gregor, Hou, Ya-Ming, Demo, Gabriel·2026·Nature Communications
DOI 10.64898/2026.01.09.698670PMC PMC12803275

Preprint — published as 10.1038/s41467-026-71781-6

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Abstract

Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli Δ rimM strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this arrested state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3’-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a significantly longer delay in recovery than other 30S maturation factors, including RbfA – the presumed primary factor in 30S maturation. Cryo-EM analysis of Δ rimM ribosomes revealed a delayed recruitment of ribosomal proteins to the 30S head domain and increased occupancy of the initiation factors IF1 and IF3, as well as recruitment of the silencing factor RsfS to the 50S subunit. These coordinated changes provide a safeguarding mechanism to block the assembly of premature 70S ribosomes. Notably, while the delayed 30S assembly in Δ rimM reduces the activity of global protein synthesis during the recovery phase, bacteria attempt to compensate for this deficiency by producing higher levels of the ribosomal machinery, indicating a programmatic change in energy allocation to generate the ribosome machinery. These findings highlight the importance of the RimM-assisted assembly of the ribosomal head domain for bacterial recovery from growth arrest.

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Metadata

Authors
Hassan, A., Nakano, Y., Gamper, H., Masuda, I., Pinkas, M., Nagarajan, S., Dworkin, J., Blaha, G., Hou, Y.-M., & Demo, G.
Affiliations
  • Central European Institute of Technology – Masaryk University (CZ)
  • Thomas Jefferson University (US)
  • Central European Institute of Technology, Masaryk University, Brno, Czech Republic
  • Columbia University (US)
  • University of California, Riverside (US)
  • Masaryk University (CZ)
Corresponding author
  • Hou, Ya-Ming
  • Demo, Gabriel
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2026-01-09
Volume
17
Issue
1
ISSN
2041-1723 (ISSN-L)
DOI
10.64898/2026.01.09.698670
PMC
PMC12803275
OpenAlex
W7153471579
Cited by
1
References
1
Citations by year
2026: 1
FWCI
2.05
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • The Medicine Forum (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • European Commission (LX22NPO5103, 90254)
  • Ministerstvo Školství, Mládeže a Tělovýchovy (90254), ID: 90254, CZ.02.01.01/00/23_015/0008175, LX22NPO5103, CZ.02.01, LM2023042)
  • Grantová Agentura České Republiky (26-20643S)
  • Central European Institute of Technology
  • National Institutes of Health
  • European Regional Development Fund (CZ.02, CZ.02.01, CZ.02.01.01/ 00/23_015/0008175, LM2023042)
  • National Institute on Aging (R21AG082005)
  • National Institute of General Medical Sciences (R35GM134931)
  • National Institute of Allergy and Infectious Diseases (R01AI139202)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
Keywords
Escherichia coli, ribosome maturation, 30S subunit, RbfA, energy allocation, ribosome biogenesis

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