Bacterial DNA repair and mutagenesis
Co-workers: Now recruiting -- visit the lab website for more information
DNA repair and mutagenesis are essential for the maintenance and plasticity of genomes in all organisms. Our research group studies these fundamental processes in bacteria, where mutagenesis underlies the evolution of antibiotic resistance. When bacterial cells are exposed to DNA damage or antibiotic treatment they launch stress responses that increase their survival. Intriguingly, these responses also upregulate mutation rates, accelerating genetic adaptation. Our recent findings show that stochasticity, or "noise", plays key roles in these responses, modulating mutation rates and diversifying cell phenotypes to evade drug treatment. Our goal is to understand the molecular processes that regulate DNA damage responses, repair, and mutagenesis and how they determine cell fates.
To this end, we take a quantitative multi-disciplinary approach. We are developing fluorescence microscopy and microfluidics methods to measure protein function at the level of single molecules in individual cells. By combining super-resolution microscopy and single-molecule tracking, we can directly watch the movement of individual proteins inside living cells.
The single-molecule analysis resolves transient protein-DNA and protein-protein interactions. With this approach, we obtain unprecedented insight into the mechanisms of DNA repair pathways in the natural cellular context.
In particular, we explore the consequences of gene expression noise and stochastic processes on the fidelity of genome maintenance. We design custom microfluidic devices to observe and manipulate single cells. Using these tools, we discovered that the activation of a bacterial DNA damage response is highly stochastic, causing cell-to-cell variation in mutation rates. Random phenotypic variation can therefore lead to heritable genetic changes. We are currently exploring how bacterial cell heterogeneity influences the efficacy of antibiotic treatment.
We also collaborate with groups at Oxford and internationally on a range of projects related to genome maintenance in bacteria and eukaryotes. Visit the lab website for more information.
Single-molecule analysis of bacterial DNA repair and mutagenesis
Uphoff S, Sherratt DJ
Annual Reviews of Biophysics, 46, 411-432 (2017)
Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P
Nature Communications, 7, 12568 (2016)
Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation
Uphoff S, Lord ND, Potvin-Trottier L, Okumus B, Sherratt DJ, Paulsson J
Science, 27290, 1094-1097 (2016)
Studying the organization of DNA repair by single-cell and single-molecule imaging
Uphoff S, Kapanidis AN
DNA Repair, 20, 32-40 (2014)
Single-molecule DNA repair in live bacteria
Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN
Proc Natl Acad Sci U S A , 110(20), 8063-8068 (2013)
In vivo architecture and action of bacterial structural maintenance of chromosome proteins
Badrinarayanan A, Reyes-Lamothe R, Uphoff S, Leake MC, Sherratt DJ
Science, 338(6106), 528-531 (2012)
DAOSTORM: an algorithm for high- density super-resolution microscopy
Holden SJ, Uphoff S, Kapanidis AN
Nature Methods, 8(4), 279-280 (2011)
Graduate Student and Postdoctoral Positions: Enquiries with CV welcome
Lab Website: http://users.ox.ac.uk/~quee2159/