Archaeal gene regulation

The tree of life, based on rRNA sequence analysis

Archaea evolved as one of the three primary lineages of life on Earth, and it was one of the major discoveries of the 20th century that they form a phylogenetic domain separate from Bacteria and Eukarya. Many characterized archaeal species are extremophiles, living in harsh and specialized habitats exposed to extremes in temperature, pH, salt concentrations. With the advent of metagenomic approaches to analyze microbial diversity, it is becoming clear that archaea are present in most common habitats and ecosystems, including oceans, soils and the human body. Despite constituting an important fraction of the biomass on Earth, archaea are still understudied and because of this, we have not yet been able to make full use of their potential for biotechnological applications.

Gene regulation is one of the most fundamental biological processes and governs cellular behaviour. The archaeal basal transcription machinery is a homologous yet simplified version of the eukaryotic RNA polymerase II system. Intriguingly, archaeal transcription factors are mostly of the bacterial type. It is therefore of great interest to unravel how these bacterial-like regulators affect transcription by interacting with the components of a eukaryotic-like basal machinery.

The central theme in the "archaea” subgroup headed by Prof. Dr. ir. Eveline Peeters is gene regulation in archaeal microorganisms in the context of their physiology. The major model organism studied is Sulfolobus acidocaldarius, which is a hyperthermoacidophile and grows optimally at 75°C and a pH of 2-4. Shown on the left is an acidic hot spring in the Azores, Portugal, which is a typical habitat of hyperthermoacidophilic archaea belonging to Sulfolobus spp.

We investigate molecular functions and mechanisms of transcription factors in the context of gene regulatory networks to learn more about how these organisms cope with ever-changing (extreme) environmental conditions. Furthermore, we aim at expanding the reach of metabolic engineering and synthetic biology beyond traditional approaches and biological platforms into archaea by exploring the use of Sulfolobus acidocaldarius as a host organism.

Selected publications

  • Peeters, E.*, Driessen, R.P.C*, Werner, F. & Dame, R.T.D. (2015). The interplay between nucleoid organization and transcription in archaeal genomes. Nature Reviews Microbiology, 13(6), 333-341.
  • Liu, H., Orell, A., Maes, D., van Wolferen, M., Lindås, A.-C., Bernander, R., Albers, S.-V., Charlier, D. & Peeters, E. (2014). BarR, an Lrp-type transcription factor in Sulfolobus acidocaldarius, regulates an aminotransferase gene in a beta-alanine-dependent manner. Molecular Microbiology, 92(3), 625-639.
  • Nguyen Duc, T., van Oeffelen, L., Song, N., Hassanzadeh-Ghassabeh, G., Muyldermans, S., Charlier, D. & Peeters, E. (2013). The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation. BMC Genomics, 14(1), 828.
  • Orell, A., Peeters, E., Jachlewski, S., Vassen, V., Schalles, S., Siebers, B. & Albers, S.-V. (2013). Lrs14 transcriptional regulators influence biofilm formation and cell motility of crenarchaea. ISME journal, 7(10), 1886-1898.
  • Peeters, E., van Oeffelen, L., Nadal, M., Forterre, P. & Charlier, D. (2013). A thermodynamic model of the interaction between the archaeal transcription factor Ss-LrpB and its tripartite operator DNA. Gene, 524(2), 330-340.
  • Lassak, K., Peeters, E., Wrobel, S. & Albers, S.-V. (2013). The one-component system ArnR: a membrane bound regulator of the crenarchaeal archaellum. Molecular Microbiology, 88(1), 125-139.
  • Peeters, E., Peixeiro, N. & Sezonov, G. (2013). Cis-regulatory logic in archaeal transcription. Biochemical Society Transactions, 41(1), 326-331.

* joint first authors