Molecular mechanisms of action by a TetR-family transcription factor in Sulfolobus acidocaldarius

Background
Archaea, however also found in mainstream habitats, are characterized by several extremophilic species. Extremophilic microorganisms have more robust proteins and unique metabolic strategies to survive extreme conditions. Sulfolobus acidocaldarius, an aerobic thermoacidophilic crenarchaeon, is a promising host for biotechnological processes.

Objectives
Getting insight in the mode of action of transcriptional mechanisms could lead to a better understanding of archaeal physiology and to an extended transcriptional toolbox for genetic engineering of Sulfolobus. Gene regulation in response to environmental conditions is crucial for the fitness and survival.
This project focuses on the characterization of a TetR-like transcription factor, SaFadR.

Methods
A variety of biochemical techniques and in vivo experiments has been implemented to study DNA-binding behaviour and physiological role.
Conclusions
By analysing the interactions of the SaFadR protein with genomic regions, SaFadR binds in vivo ten genomic regions, with the highest affinity to its own promoter region and the one of a juxtaposed, divergently transcribed operon. Other ChIP-seq binding peaks were observed for an operon encoding enzymes involved in the β-oxidation pathway. This binding is confirmed in vitro by performing EMSA. Addition of a fatty acyl-CoA reduces the in vitro binding.
Using a SaFadR knockout strain, the relative expression levels of SaFadR and the other possible target genes were compared with an isogenic wild type by qRT-PCR.
Based on these results we can conclude that the SaFadR protein is a fatty acid responsive transcription factor that represses genes involved in fatty acid and lipid metabolism in a fatty acyl-CoA dependent manner.