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Structural analysis of the bacterial DNA replication machinery

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  • Full or part time
    Dr M Lamers
  • Application Deadline
    Applications accepted all year round

Project Description

Contact for application enquiries – [email protected]
Contact for project enquiries - [email protected]
PhD start date – 25th September 2017

Three year studentship, fully funded for EU/UK students by the Department of Molecular and Cell Biology (College of Medicine, Biological Sciences and Psychology)

Deadline – applications will be accepted until the position is filled

Project title: Structural analysis of the bacterial DNA replication machinery

Supervisor: Professor Meindert Lamers

Project description
Faithful replication of genomic DNA is essential to all organisms. However, DNA replication is greatly complicated by the two strand of the DNA that run in opposite direction. Therefore, as the replication machinery is moving along the DNA, one strand is copied in one continuous stretch of more than 100,000 base pairs while the other strand is synthesized in a discontinuous manner with fragments sizes of up to 1000 base pairs. The simultaneous replication of both strandsis performed by a large assembly of 12 different proteins called theDNA polymerase III holoenzyme. This large complex catalyzes several events such as DNA unwinding by the DNA helicase, RNA primer synthesis by the primase, clamp loading by the clamp loader complex, DNA synthesis by the polymerase, and proofreading by the exonuclease. Structures of the individual proteins are known, but no structural information is available on the complete holoenzyme. With modern cryo-EM techniques and biochemical trapping of stable states we are now able for the first time to study the structure of the intact holoenzyme.

The aim of the PhD project is therefore to study the structural features of the complete DNA polymerase III holoenzyme. For this the student will be using different structural techniques, such as cryo electron microscopy, protein crystallography, small angle X-ray scattering as well as diverse biochemical techniques.

Funding Notes

Funded PhD project (European/UK students only)


Self-correcting mismatches during high-fidelity DNA replication. (2017) Fernandez-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH. Nat Struct Mol Biol. 24, 140-143.

Fernandez-Leiro R, Conrad J, Scheres HWS and Lamers MH. (2015) Cryo-EM structures of the E. coli replicative DNA polymerase reveal dynamic interactions with clamp, exonuclease and τ. eLife 4:e11134

Rock JM, Lang UF, Chase MR, Ford CB, Gerrick ER, Gawande R, Coscolla M, Gagneux S, Fortune SM and Lamers MH. (2015) Replication fidelity in M. tuberculosis is mediated by an ancestral prokaryotic proofreader. Nature Genetics 47, 677-681

Toste Rêgo A, Holding A, Kent H and Lamers MH. (2013) Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J. 32, 1334-43

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