DNA bases in all cells are damaged by erroneous methylation events and methylated bases must be repaired in order to avoid mutations and other harmful effects. Single-step direct reversal of methylation damage is one of the most cost-effective and efficient DNA repair pathways known. The E. coli enzyme involved in DNA repair of methylated bases such as 1-methyladenine and 3-methylcytosine is known as AlkB. Homologs of E. coli AlkB have been found in many bacteria, in viruses and in eukaryotes. In human cells, nine AlkB homologs have been detected, hALKBH1-8 and hFTO.
hALKBH2 and hALKBH3 are fairly well-characterized proteins and have been shown to repair methylated bases in human cells. hALKBH8 has recently been shown to be involved in modifications of tRNA wobble position uridines. The 3D structures of E. coli AlkB and human ALKBH2/3 have been determined experimentally, but the structure of the other human AlkB homologs is at present unknown. The biological function of hALKBH1, hALKBH4-7, and hFTO is at present either unknown or controversial.
This project is mainly intended for a student with a particular interest in biology, who wish to use informatics methods and bioinformatics tools to solve problems in applied molecular biology.
The following structural bioinformatics master thesis project is suggested
- Generate 3D models of hALKBH1-8 of the apo enzymes and the enzymes bound to DNA by comparative modelling based on published experimental structures
- Focus in particular on modelling the “lid-like” structure that is covering the substrate and active site in the experimental structures
- Collect sequence data for hALKBH1-8 homologs in vertebrates and other eukaryotes from public data at the NCBI, the Ensembl project and various sequencing centre websites
- Based on the sequence data, study the phylogeny of the AlkB family in Eukaryota, Metazoa and/or vertebrates
- Use the 3D models and phylogenetic data in order to elucidate the function of hALKBH1-8, for example by suggesting substrates and interaction sites and by investigating conserved and variable segments, motifs, and residues
- It is expected that this will provide valuable input for ongoing experimental work on these enzymes in several groups at UiO/Rikshospitalet
- The project may be extended to include other, more remote, human AlkB homologs that recently have been shown to be involved in processing DNA bases, namely FTO (obesity associated) and TET1-3 (oxidation of epigenetically marked 5-methylcytosine)
Work from our group involves comparative modelling of a new superfamily of DNA repair enzymes, a review on DNA base damage recognition and processing, and two studies on AlkB homologs Abh1 and Ofd2 from the fission yeast Schizosaccharomyces pombe.
Supervisor: Research Scientist Jon K. Lærdahl, Department of Medical Microbiology, Oslo University Hospital, Rikshospitalet & BMI, IFI, UiO; e-mail: jonkl@medisin.uio.no; Tel.: 99507335
Please contact Jon for further details and clarifications