Protein-DNA interactions at atomic levels

---

Project leader: Dr Elin Moe og Prof. Arne O. Smalås


DNA-binding proteins are amongst the most frequently occurring proteins found in the genomes of bacteria, archea and eukaryotes.

The recent advances in genome sequencing, coupled with the development of powerful computer algorithms for homology comparison and the prediction of structural elements from sequence data has led to the detection of many new DNA-binding proteins, many of them with unknown function. There appears to exist a limited number of different DNA-binding motifs that are the primary recognition site of DNA (the DNAProt database currently lists 33 classes of DNA-binding motifs), but the detailed binding mechanisms and the origin of the variation in DNA sequence specificity is not well understood for most of the classes.

In order to increase the understanding of the biochemical and molecular basis for protein-DNA interaction want to identify and investigate new DNA-interacting enzymes from Deinococcus radiodurance, and Vibrio salmonicida with possible new catalytic features and specificities

Model systems for Protein-DNA interactions

Vibrio salmonicida
A halophilic (“salt-loving”) and psychrophilic (“cold-loving”), curved gram-negative rod bacterium that is the causative agent of cold-water vibriosis (also called hemorrhagic syndrome or the Hitra disease) in Atlantic cod and salmon. Although the entry route is still largely unknown, V. salmonicida elicits tissue degradation, hemolysis and sepsis. Vaccines against the disease have been developed but the molecular mechanisms of host invasion and specificity are yet unknown. The genome of V. salmonicida is currently being sequenced and annotated as an initiative between the University of Tromsø and the Wellcome Trust Sanger Institute.

Deinococcus radiodurance
A gram-positive bacterium, which exhibits a tremendous resistance to ionising radiation and is efficiently able to repair about 150 double strand breaks in its genome without detectable loss of viability. The annotated sequence of the D. radiodurans genome was published in 1999 and allowed a detailed analysis of the composition of this organism, however the exact mechanisms of damage repair remain unclear.

Aim for the Protein-DNA interaction studies


The main goal is to expand our knowledge about protein-DNA interactions at an atomic level by identification and investigation of novel DNA-interacting proteins from D. radiodurans and V. salmonicida. By characterisation of already known DNA glycosylases from these organisms we will establish new protein-DNA interaction characterisation technology. Biochemical data of the novel proteins will be needed in order to select proteins with unique features of commercial interest.
This a collaboration between NorStruct and the macro molecular crystallography group at ESRF in Grenoble, France.

Publications

Moe, E., Leiros, I., Smalås, A.O. and McSweeney, S. (2005) The crystal structure of mismatch specific uracil-DNA glycosylase (MUG) from Deinococcus radiodurans revels a noveal catalytic residue and broad substrate specificity. J. Biol. Chem. 281(1):569-577.

Leiros I, Moe E, Smalås AO and McSweeney S. (2005) Structure of the uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans. Acta Crystallogr D Biol Crystallogr. 61:1049-56.

Leiros I, Timmins J, Hall DR, McSweeney S. (2005) Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. EMBO J. 24(5):906-18.

Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalås A and Willassen NP. (2004) Optimisation of the surface electrostatics as a strategy for cold adaptation of uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). J Mol Biol. 343(5):1221-30.

Leiros I, Moe E, Lanes O, Smalås AO and Willassen NP. (2003) The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features. Acta Crystallogr D Biol Crystallogr. 59:1357-1365.