---
OA_place: publisher
OA_type: hybrid
_id: '19857'
abstract:
- lang: eng
text: Bacteria have evolved a wide range of defence strategies to protect themselves
against bacterial viruses (phages). Most known bacterial antiphage defence systems
target phages with DNA genomes, which raises the question of how bacteria defend
against phages with RNA genomes. Bacterial toxin–antitoxin systems that cleave
intracellular RNA could potentially protect bacteria against RNA phages, but this
has not been explored experimentally. In this study, we investigated the role
of a model toxin–antitoxin system, MazEF, in protecting Escherichia coli against
two RNA phage species. When challenged with these phages, the native presence
of mazEF moderately reduced population susceptibility and increased the survival
of individual E. coli cells. Genomic analysis further revealed an underrepresentation
of the MazF cleavage site in genomes of RNA phages infecting E. coli, indicating
selection against cleavage. These results show that, in addition to other physiological
roles, RNA-degrading toxin–antitoxin systems may also help defend against RNA
phages.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: This work was supported by ISTFELLOW (People Program – Marie Curie
Actions of the European Union’s Seventh Framework Program FP7 under REA grant agreement
291734), the FWF (Austrian Science Fund) Elise Richter Program project number V
738 and the Wellcome Trust Institutional Strategic Support Award (WT105618MA), to
N.N. M.P. was a Simons Foundation Fellow of the Life Sciences Research Foundation.
We are grateful to Kathrin Tomasek, Lisa Butt, Chris Estell, Alys Jepson, Franklin
Nobrega, Stefano Pagliara, Remy Chait, Steve West, Vicki Gold, Josh Eaton, Ivana
Gudelj and Rob Beardmore for useful discussions and technical support, as well as
to Robin Wright, Christian Fitch and Ben Temperton for sharing equipment. We thank
Laurence Van Melderen for sharing the strains. We acknowledge the IST Austria Lab
Support Facility, LSI Technical Services Team at the University of Exeter and the
Translational Research Exchange @ Exeter (TREE) network. N.N. is grateful to Fabrice
Gielen for his support.
article_number: '20250080'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Nikolic N, Pleska M, Bergmiller T, Guet CC. A bacterial toxin-antitoxin system
as a native defence element against RNA phages. Biology Letters. 2025;21(6).
doi:10.1098/rsbl.2025.0080
apa: Nikolic, N., Pleska, M., Bergmiller, T., & Guet, C. C. (2025). A bacterial
toxin-antitoxin system as a native defence element against RNA phages. Biology
Letters. The Royal Society. https://doi.org/10.1098/rsbl.2025.0080
chicago: Nikolic, Nela, Maros Pleska, Tobias Bergmiller, and Calin C Guet. “A Bacterial
Toxin-Antitoxin System as a Native Defence Element against RNA Phages.” Biology
Letters. The Royal Society, 2025. https://doi.org/10.1098/rsbl.2025.0080.
ieee: N. Nikolic, M. Pleska, T. Bergmiller, and C. C. Guet, “A bacterial toxin-antitoxin
system as a native defence element against RNA phages,” Biology Letters,
vol. 21, no. 6. The Royal Society, 2025.
ista: Nikolic N, Pleska M, Bergmiller T, Guet CC. 2025. A bacterial toxin-antitoxin
system as a native defence element against RNA phages. Biology Letters. 21(6),
20250080.
mla: Nikolic, Nela, et al. “A Bacterial Toxin-Antitoxin System as a Native Defence
Element against RNA Phages.” Biology Letters, vol. 21, no. 6, 20250080,
The Royal Society, 2025, doi:10.1098/rsbl.2025.0080.
short: N. Nikolic, M. Pleska, T. Bergmiller, C.C. Guet, Biology Letters 21 (2025).
corr_author: '1'
date_created: 2025-06-22T22:02:06Z
date_published: 2025-06-11T00:00:00Z
date_updated: 2025-09-30T13:38:08Z
day: '11'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1098/rsbl.2025.0080
ec_funded: 1
external_id:
isi:
- '001505019800001'
pmid:
- '40494395'
file:
- access_level: open_access
checksum: 016f644ed068f8609ded306ad26dbd3f
content_type: application/pdf
creator: dernst
date_created: 2025-06-23T11:34:39Z
date_updated: 2025-06-23T11:34:39Z
file_id: '19873'
file_name: 2025_BiologyLetters_Nikolic.pdf
file_size: 1850797
relation: main_file
success: 1
file_date_updated: 2025-06-23T11:34:39Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 26956E74-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00738
name: Bacterial toxin-antitoxin systems as antiphage defense mechanisms
publication: Biology Letters
publication_identifier:
eissn:
- 1744-957X
issn:
- 1744-9561
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A bacterial toxin-antitoxin system as a native defence element against RNA
phages
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2025'
...
---
_id: '9410'
abstract:
- lang: eng
text: Antibiotic concentrations vary dramatically in the body and the environment.
Hence, understanding the dynamics of resistance evolution along antibiotic concentration
gradients is critical for predicting and slowing the emergence and spread of resistance.
While it has been shown that increasing the concentration of an antibiotic slows
resistance evolution, how adaptation to one antibiotic concentration correlates
with fitness at other points along the gradient has not received much attention.
Here, we selected populations of Escherichia coli at several points along a concentration
gradient for three different antibiotics, asking how rapidly resistance evolved
and whether populations became specialized to the antibiotic concentration they
were selected on. Populations selected at higher concentrations evolved resistance
more slowly but exhibited equal or higher fitness across the whole gradient. Populations
selected at lower concentrations evolved resistance rapidly, but overall fitness
in the presence of antibiotics was lower. However, these populations readily adapted
to higher concentrations upon subsequent selection. Our results indicate that
resistance management strategies must account not only for the rates of resistance
evolution but also for the fitness of evolved strains.
acknowledgement: We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton,
Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall,
Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and
Michael Whitlock for insightful support.
article_number: '20200913'
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913
apa: Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points
along antibiotic concentration gradients. Biology Letters. Royal Society
of London. https://doi.org/10.1098/rsbl.2020.0913
chicago: Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different
Points along Antibiotic Concentration Gradients.” Biology Letters. Royal
Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.
ieee: M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along
antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal
Society of London, 2021.
ista: Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic
concentration gradients. Biology letters. 17(5), 20200913.
mla: Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration
Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of
London, 2021, doi:10.1098/rsbl.2020.0913.
short: M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).
corr_author: '1'
date_created: 2021-05-23T22:01:43Z
date_published: 2021-05-12T00:00:00Z
date_updated: 2026-04-02T14:02:44Z
day: '12'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsbl.2020.0913
ec_funded: 1
external_id:
isi:
- '000651501400001'
pmid:
- ' 33975485'
file:
- access_level: open_access
checksum: 9c13c1f5af7609c97c741f11d293188a
content_type: application/pdf
creator: kschuh
date_created: 2021-05-25T14:09:03Z
date_updated: 2021-05-25T14:09:03Z
file_id: '9425'
file_name: 2021_BiologyLetters_Lagator.pdf
file_size: 726759
relation: main_file
success: 1
file_date_updated: 2021-05-25T14:09:03Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Biology letters
publication_identifier:
eissn:
- 1744-957X
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptation at different points along antibiotic concentration gradients
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 17
year: '2021'
...
---
_id: '6467'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized
by some large epistatic effects, these data give a good overall fit to the non-epistatic
null model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
article_number: '0881'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes.
Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881
apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple
fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881
chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis
on Simple Fitness Landscapes.” Biology Letters. Royal Society of London,
2019. https://doi.org/10.1098/rsbl.2018.0881.
ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness
landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London,
2019.
ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness
landscapes. Biology Letters. 15(4), 0881.
mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple
Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society
of London, 2019, doi:10.1098/rsbl.2018.0881.
short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019).
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2025-07-10T11:53:23Z
day: '03'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rsbl.2018.0881
ec_funded: 1
external_id:
isi:
- '000465405300010'
pmid:
- '31014191'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2018.0881
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biology Letters
publication_identifier:
eissn:
- 1744-957X
issn:
- 1744-9561
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4461008
record:
- id: '9799'
relation: research_data
status: public
- id: '9798'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The distribution of epistasis on simple fitness landscapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2019'
...