Most genes of prokaryotes are organized in operons. Genes that reside in operons in bacteria and archaea are co-transcribed as one poly-cistronic messenger RNA (mRNA). The operon organization allows for co-regulated gene expression which is advantageous when equimolar amounts of gene products are required, for instance to generate multi-subunit complexes with an even stoichiometry. However, a substantial number of multi-subunit complexes have an uneven stoichiometry. The production of these protein complexes with an uneven stoichiometry requires specific tuning mechanisms to generate subunits in appropriate relative quantities.
We aim at discovering the mechanisms by which differential protein production of operon encoded complexes is regulated.
Using comparative analysis of bacterial and archaeal genomes, we have show that differential translation is a key determinant of modulated expression of genes that are clustered in operons. A comprehensive analysis of transcript sequence features has shown that codon bias generally is the best in silico indicator of unequal protein production. In addition, we have obtained experimental evidence that de novo initiation of translation can occur at inter-cistronic sites, allowing for differential translation of any gene irrespective of its position on a poly-cistronic messenger. Thus, modulation of translation efficiency appears to be a universal mode of genome expression control in bacteria and archaea that provides for tuned production of operon-encoded proteins.
The next step would be to test which factors are exactly responsible for differential translation rates of genes in operons. Codon bias, influencing translation elongation and mRNA secondary structure, influencing translation initiation are the two main candidates. This project could involve either a bioinformatics analysis of codon usage and mRNA structure in prokaryotic genomes, or wet lab experiments aiming at testing hypotheses derived from in silico studies, in vivo using GFP constructs in E. coli as a model. A combination of both is possible as well, depending on your individual interests.
Project for MSc student with interest in Microbiology
Supervision: John van der Oost, PhD
Laboratory of Microbiology
Microbiology building (316)
Duration: 4 months minimum