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BP: Fachverband Biologische Physik

BP 24: Systems biology

BP 24.2: Talk

Wednesday, April 2, 2014, 10:00–10:15, ZEU 250

A model for sigma factor competition in bacterial cells — •Marco Mauri and Stefan Klumpp — Max Planck Institute of Colloids and Interfaces, Potsdam, Germany

Bacteria respond to changing environment conditions by switching the global pattern of transcribed genes, making only those products essential for their survival. In response to specific environmental stresses, the cell activates several stress-specific molecules called sigma factors. They bind the core RNA polymerase and direct it towards the appropriate stress response genes. Since more than one sigma species could be present in the cell at the same time, it is believed that the modulation of their availability and competition among them for core RNAP provide important mechanisms for the global switch of the transcriptional program. To analyze this competition, we developed a theoretical model based on earlier work from the Gross lab. Within this framework, we inspect the effects of some factors that modulate the competition such as anti-sigma factors, small RNA, active transcription and non-specific binding. The model shows that a passive regulation of the transcription of the alternative sigma cognate genes is feasible and a more effective upregulation is achieved in competition regime. We also examine under which conditions a stop of transcription of ribosomal RNA as in the stringent response can passively up-regulate transcription driven by alternative sigmas. Our model matches well to in vitro and in vivo measurements here analyzed. The theory supports evidence for a passive global switch of the transcriptional program and gives new insights into RNAP partitioning in the cell.