What causes cellular heterogeneity?
Degradation of LexA repressor leads to spontaneous activation of the SOS DNA damage response.
How do DNA-binding proteins search for their target sites in cells?
The bacterial chromosome is crowded with proteins that bind transiently to non-specific sites.
Real-time dynamics of mutagenesis
...reveal the chronology of DNA repair and damage tolerance responses in single cells.
Bad luck and mutations
Stochastic DNA damage response causes cell-to-cell mutation rate variation.
Single-molecule DNA repair in live bacteria
Using photoactivated single-molecule tracking to directly follow individual DNA repair proteins in living E. coli cells.
Methods for single-molecule imaging
Custom single-molecule fluorescence microscopes, imaging methods, and software.
DNA repair, Mutation, and Stress Adaptation in Bacteria
Bacteria have a remarkable capacity to thrive in adverse environments. Their adaptability relies on stress responses that provide temporary protection, for example by repairing cell damage or removing toxic chemicals. Such phenotypic adaptation offers cells a window of opportunity to evolve permanent stress resistance through genetic change. Failures to cure bacterial infections with antibiotics are often due to stress responses that promote bacterial survival as well as the evolution of drug resistance. Our lab seeks to understand how this works at the molecular level using a quantitative interdisciplinary approach. We focus on the mechanisms of DNA repair and mutagenesis, which are essential both for stress survival and for genetic change. A key aspect of our research is developing fluorescence microscopy techniques to visualise molecular events in real-time within living cells. We use super-resolution microscopy and single-molecule tracking to record the localization and movement of individual molecules such as DNA repair enzymes or transcription factors. To monitor the cellular responses to stress, we use microfluidic devices for imaging single cells. This allows us to decipher how molecular events inside cells determine long-term cell fates. Curiously, single-cell analysis revealed that bacterial phenotypes are variable even in a constant environment, a phenomenon that may be linked to stress survival. We discovered that mutation rates are also variable due to fluctuations in the expression of DNA repair proteins. These findings open fundamental questions about the mechanisms and regulation of mutagenesis, which we are now addressing using a range of novel microscopy and genetic approaches.
Uphoff Lab | Department of Biochemistry | University of Oxford
News
Chaotic behaviour
December 2023
Single bacteria exhibit chaotic oscillations in gene expression in response to oxidative stress. Our new study in Current Biology demonstrates that chaos exists in biological systems and may play a role in stress adaptation of cell populations.
A burst of mutations
November 2022
Cell stress triggers phenotypic and genetic changes. Our paper in EMBO Reports shows how stress responses modulate mutation rate dynamics: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress.
Phenotypic heterogeneity driven by cell-cell interactions
September 2022
Divya's paper in Cell Reports shows that Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions
Genetic plasticity meets DNA repair heterogeneity
December 2021
Variation in DNA repair protein expression leads to differences in mutation rates between cells. Article now published in Nucleic Acids Research: Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity.
DNA interstrand crosslink repair visualised in cells
June 2023
Our lab contributed to a paper by Martin Cohn's group on the regulation of DNA interstrand crosslink repair, now published in Cell Reports: Phosphorylation by ATR triggers FANCD2 chromatin loading and activates the Fanconi anemia pathway
Book chapter
August 2022
Chloe Cassaro's chapter in the series Methods in Molecular Biology includes a detailed point-by-point protocol for Super-Resolution Microscopy and Tracking of DNA-Binding Proteins in Bacterial Cells
LexA and the SOS response
June 2021
Bacteria sometimes induce the SOS DNA damage response even in the absence of stress. Why this happens and other findings revealed by a single-molecule tracking approach described in our new paper in Nature Microbiology. Free access: Imaging LexA degradation in cells explains regulatory mechanisms and heterogeneity of the SOS response.
DNA-target search
February 2021
Our new article in Molecular Cell shows that the bacterial chromosome is crowded with non-specifically bound proteins. Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.
Clara Kummerer and Tendai Makamure
September 2023
Clara and Tendai have joined our team for their Part ii research projects.
Claire Qu
June 2023
Welcome to Claire Qu for her summer internship funded by the Lister Institute.
Fiona Sargison
October 2022
Welcome to Fiona Sargison who moved from Edinburgh to start a postdoc in our group.
DNA organization - replication - segregation
August 2021
Interplay between chromosome organization and replication fosters non-random inheritance of genetic material. Article now published in PNAS: Non-random segregation of sister chromosomes by Escherichia coli MukBEF.
Colworth Medal Lecture
April 2021
Watch Stephan's award lecture for the Biochemical Society Colworth medal on youtube: Seeing DNA repair and mutagenesis in bacteria.