Cryo-EM reveals multiple mechanisms of ribosome inhibition by doxycycline
Posted on: 6 January 2026 , updated on: 7 January 2026
Preprint posted on 9 November 2025
Categories: biochemistry, cell biology, microbiology, molecular biology, pharmacology and toxicology
Background
As a society, we are facing a crisis the extent of which can only be guessed at, but certainly cannot be predicted: antimicrobial resistance and the failure of our traditional antibiotics. That is why it is now more important than ever to efficiently search for new antibiotics with new mechanisms of action.
Coxiella burnetii (C. burnetii), a highly contagious zoonosis, is considered a major risk to public health, especially for humans who work closely with animals, such as butchers, farmers, and veterinarians, with inhalation being the predominant route of infection. Infection with C. burnetii leads to Q-fever, which in its acute stage is accompanied by fever, chills, and headache and is associated with secondary diseases such as hepatitis, chronic fatigue, and endocarditis [2]. In 1-5% of patients, infection can take a chronic course, which usually occurs 2 years after infection [1]. What makes the bacterium itself so dangerous is its dormant stage and its associated biphasic lifecycle, which allows the bacterium to survive for a long time in a “spore stage” [3].
Infection with Coxiella burnetii is treated with the antibiotic doxycycline, which has a low minimum inhibitory concentration (MIC) of 0.05 mg/L against Coxiella burnetii [4]. Doxycycline acts in the classic manner by targeting the bacterial ribosome, blocking the binding of tRNA to the A site by binding to the canonical tetracycline binding site within the ribosomal A site.
Using cryo-EM imaging, the group demonstrates two new mechanisms of action for doxycycline. While doxycycline blocks the exit tunnel of the large ribosomal subunit in Coxiella burnetii, doxycycline causes significant conformational changes within the peptide transfer centre, the catalytic core of the ribosome, in E. coli, blocking tRNA binding.
Key Findings
Hibernation factor HPFcold protects ribosomes via binding to the 16S anti-Shine Dalgarno Sequence
They identified the position of one of five hibernation factors, HPFcold, (described in the preprint: The evolutionary lifecycle of ribosome hibernation factors, DOI:
https://doi.org/10.1101/2025.11.04.686544) which comprises an N-terminal domain harbouring a sigma-54 fold and a cold sock domain fold (CSD) positioned at the C terminal. This CSD domain binds to the aSD sequence via hydrogen bonding and stacking interactions, limiting RNase binding to the ribosome. The ribosome therefore remains active and functional despite extended hibernation periods. This finding thus describes the first validation of a hibernation factor and its function. Although there are sequence similarities of HPFcold and other CSDs, the proteins clearly differ from one another, with similar structure but likely different functions.
Identification of a new large ribosomal protein called CLaSP
Electron density analyses revealed the existence of a previously unknown ribosomal protein, termed Coxiellaceae Large Subunit Peptide (CLcSP), part of the large ribosomal subunit. Although the exact function of CLaSP is still unknown, it is thought to play a role in the correct assembly of the ribosome, as CLaSP stabilizes the ribosome via anchoring of s23S and r5S.
Doxycycline molecules stack within the ribosomal exit tunnel of the 50S subunit, blocking peptide exit extensively
Analysis revealed a stack of three Doxycycline molecules blocking the peptide exit tunnel between bases U2606 and C2631, which sense ribosomal stalling and translational arrest. The stack is arranged around three magnesium ions, facilitated by the arrangement of the molecules in relation to each other. Although blocking the exit tunnel is not a new mechanism of action per se, the extensive blocking facilitated due to molecule stacking is considered a new phenomenon, which can be traced back to the size of the tetracyclines. The authors therefore suggest, that this mechanism of action can only be performed by smaller tetracyclines, which means that the strong effect of Doxycycline and the low MIC can be attributed to the efficient binding of the large ribosomal subunit.

Preprint Figure 4: Graphical representation of extensive blocking of the peptide exit tunnel via stacking of three Doxycycline molecules numbered by increased distance to the peptidyl transferase centre: DOX1, DOX2 and Dox 3.
Doxycycline binding induces structural rearrangements of E. Coli peptidyl transferase centre and early exit tunnel
Contrary to prevailing expectations, cryo-EM analysis indicates that the peptidyl transferase center (PTC) is less static than previously assumed. Doxycycline binding disrupts the essential A2450–C2063 interaction required for proper tRNA accommodation and renders residues 60–65 of the bL4 loop disordered, further compromising translational fidelity. In this doxycycline-bound, “zipped” ribosome state, the combined conformational changes are likely to inactivate the ribosome and abolish translation.
Why I highlight this work
Antibiotic resistance is becoming an ever-greater threat, which makes the development of new antibiotics all the more urgent. For this, however, it is crucial to understand in detail how antibiotics work and how these mechanisms can be leveraged therapeutically. What I find particularly striking in this paper is that even long-established antibiotics such as doxycycline can still reveal previously unrecognized mechanisms of action that may be pharmacologically important. At the same time, the study also exposes the weaknesses of some next-generation agents: doxycycline remains more potent than newer compounds like tigecycline or eravacycline.
Findings like these give hope that antibiotic design will become increasingly rational in the future, as we continue to learn which molecular properties are essential for successful therapy, including aspects as simple, yet impactful, as molecular size. I also think it is important to acknowledge that even long-held paradigms may turn out to be incomplete. This work clearly demonstrates that the peptidyl transferase centre is not as static as often assumed, but in fact capable of notable rearrangements.
And even if ribosomes or antibiotic mechanisms are not your primary interest, the paper is worth reading for its cryo-EM visualizations alone, the structural representations of the ribosome are genuinely impressive.
References:
[1] Sheila B Buijs, Chantal P Bleeker-Rovers, Sonja E van Roeden, Linda M Kampschreur, Andy I M Hoepelman, Peter C Wever, Jan Jelrik Oosterheert, Still New Chronic Q Fever Cases Diagnosed 8 Years After a Large Q Fever Outbreak, Clinical Infectious Diseases, Volume 73, Issue 8, 15 October 2021, Pages 1476–1483, https://doi.org/10.1093/cid/ciab476
[2] Million M, Raoult D. No Such Thing as Chronic Q Fever. Emerg Infect Dis. 2017 May;23(5):856-857. doi: 10.3201/eid2305.151159. PMID: 28418317; PMCID: PMC5403045.
[3] Eldin C, Mélenotte C, Mediannikov O, Ghigo E, Million M, Edouard S, Mege JL, Maurin M, Raoult D. From Q Fever to Coxiella burnetii Infection: a Paradigm Change. Clin Microbiol Rev. 2017 Jan;30(1):115-190. doi: 10.1128/CMR.00045-16. PMID: 27856520; PMCID: PMC5217791.
[4] Lever MS, Bewley KR, Dowsett B, Lloyd G. In vitro susceptibility of Coxiella burnetii to azithromycin, doxycycline, ciprofloxacin and a range of newer fluoroquinolones. Int J Antimicrob Agents. 2004 Aug;24(2):194-6. doi: 10.1016/j.ijantimicag.2004.05.001. PMID: 15288324.
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| List by | Barbora Knotkova et al. |
Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate
This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2025. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.
| List by | Virginia Savy, Martin Estermann |
April in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics
| List by | Vibha SINGH et al. |
Biologists @ 100 conference preList
This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.
| List by | Reinier Prosee, Jonathan Townson |
February in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry and cell metabolism 2) cell organelles and organisation 3) cell signalling, migration and mechanosensing
| List by | Barbora Knotkova et al. |
Community-driven preList – Immunology
In this community-driven preList, a group of preLighters, with expertise in different areas of immunology have worked together to create this preprint reading list.
| List by | Felipe Del Valle Batalla et al. |
January in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression
| List by | Barbora Knotkova et al. |
2024 Hypothalamus GRC
This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.
| List by | Nathalie Krauth |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | Alex Eve, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
| List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
| List by | Nadja Hümpfer et al. |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | Madhuja Samaddar et al. |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
| List by | Sandra Franco Iborra |
Also in the pharmacology and toxicology category:
April in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics
| List by | Vibha SINGH et al. |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
COVID-19 / SARS-CoV-2 preprints
List of important preprints dealing with the ongoing coronavirus outbreak. See http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic
| List by | Dey Lab, Zhang-He Goh |
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Drug use in special populations
Any drugs that are being used in special populations: Patients with liver and kidney failure, in paediatrics, in geriatrics, and in pregnant or lactating patients. Includes the discovery of factors that could potentially affect drug use in these special populations.
| List by | Zhang-He Goh |
Toxicology of toxicants, existing therapeutics, and investigational drugs
Preprints that describe the toxicology of environmental pollutants and existing and upcoming drugs. Includes both toxicokinetics and toxicodynamics, as well as technological improvements that will help in the characterisation of this field.
| List by | Zhang-He Goh |
Antimicrobials: Discovery, clinical use, and development of resistance
Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.
| List by | Zhang-He Goh |
Anticancer agents: Discovery and clinical use
Preprints that describe the discovery of anticancer agents and their clinical use. Includes both small molecules and macromolecules like biologics.
| List by | Zhang-He Goh |
Advances in Drug Delivery
Advances in formulation technology or targeted delivery methods that describe or develop the distribution of small molecules or large macromolecules to specific parts of the body.
| List by | Zhang-He Goh |






