Centre for Molecular and Biomolecular Informatics Radboud University, Toernooiveld 1, P.O. Box 9010, 6500 GL Nijmegen, +31 (0)24-3653391, postmaster@cmbi.ru.nl

With the sequencing of complete genomes we can predict the metabolic pathways in a species. Some of these species are of particular importance, either for medical or for industrial reasons. The Pyrococci are a genus that belong to the so-called "Archaea", one of the three branches in the evolution of cellular life, and the one about which the least is known. Pyrococci life at about 90 C. They have a large "reductive" potential and are therewith of interest for the production of certain fine chemicals (alcohols and aldehydes) from carboxyl acids. The goal of this project is to detect the enzymes that are involved in the carbohydrate metabolism (e.g. glycolysis, citric acid cycle, fatty acid metabolism) of the Pyrococci. Some of them have already been annotated in the genome, but with the methods that are being developed in our group we can propose new ones. This project is in direct collaboration with the experimental group of John van der Oost, Univ. Wageningen, where specific predictions can be tested.

Methodology

This project involves a combination of homology searches (prediction protein function by detecting similarity with experimentally characterized proteins), and context searches (detecting the functional context of a protein, e.g. the pathway in which it is involved, by looking at its context in the genome). These techniques will be thought during the stay in the group.

Required pre-training

Interest and affinity with metabolic pathways, including a basic knowledge of biochemistry, is required.

Keywords: Comparative genomics, metabolic pathway, carbohydate metabolism.

Training period: 6-12 months

Information: Martijn Huynen, huynen@cmbi.kun.nl, tel 024-3653374.