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

The goal of this project is to delineate which proteins function in the mitochondria, and what are the functional interactions between them. Various types of data are available about the protein complement of mitochondria. They include experimental data like the ones resulting from proteomics or from genome sequencing. We would like to predict how these proteins interact with each other to form pathways and protein complexes. In order to do that we will map the evolution of the mitochondrial proteome. Proteins whose genes show a strong genomic association, e.g. because they tend to be lost from the genome together, are predicted to functionally interact with each other

Objectives

This project involves comparison of the complete genomes of close relatives of the Bacterial ancestors of the mitochondria e.g., Rickettsia prowazekii, Rickettsia conorii, Caulobacter crescentus as well as genomes of the eukaryotes Homo sapiens, Saccharomyces cerevisiae, Arabidopsis thaliana, Encephalotozoon cuniculi, Caernohabditis elegans and Drosophila melanogaster . The main objectives are:

1. Comparing the bacterial genomes with those of the eukaryotes to infer which eukaryotic genes have been derived from the alpha-proteobacteria.
2. Comparing the organization of conserved genes (e.g. pairs, clusters, operons) in the alpha-proteobacteria, and use that information to predict functional interactions between their proteins.
3. Comparing the eukaryotic genomes with each other to find which proteins have been lost during the mitochondrial evolution, using instances of coordinated loss of genes to predict functional interactions between their proteins.

Required pre-training

The student should have a background in (bio)chemistry with interest and knowledge of metabolic pathways.

Keywords: Comparative genomics, genome evolution, multiple sequence alignment, mitochondria, metabolic pathways.

Training period: 6-12 months

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