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D 1 - Hannes Link

Sensing of carbon starvation through the metabolic network and the stringent response system

Dr. Hannes Link
SYNMIKRO & Max Planck Institute for Terrestrial Microbiology

Karl-von-Frisch-Strasse 16
35043 Marburg

Phone: +49 - 6421 - 2821624

Research summary

A most critical, yet frequent change in the environment of bacteria is the depletion of carbon sources. The physiological changes upon carbon limitation and starvation are commonly referred to as the stringent response, which centres on the second messengers guanosine tetraphosphate and guanosine pentaphosphate (collectively (p)ppGpp). Although functioning of the stringent response is well characterized at the level of gene regulation, its impact on metabolism remains poorly understood.

In this project we will examine the metabolic changes triggered through the stringent response. We have recently measured metabolic changes in nucleotide and amino acid metabolism during the switch between starvation and growth, and observed dynamics with characteristic timing upon entry and exit from starvation (I). The regulatory mechanisms that were responsible for these dynamics, included feedback inhibition of amino acids and supply driven activation of nucleotide pathways. However, we did not examine the role of the stringent response in the observed metabolic changes. Here, we will investigate how carbon starvation is sensed through the metabolic network and the stringent response system. Therefore we subdivided this project into the following three objectives:

  • Objective 1
    Evolving populations of Escherichia coli under different conditions of carbon starvation using a parallel bioreactor system.

  • Objective 2
    Metabolic analysis of the evolved populations using high throughput metabolomics, and linking metabolic phenotypes to mutations in components of the stringent response (specifically gene regions of rpoS, spoT and relA). We will also consider unbiased approaches to find genetic changes across the whole genome using pool sequencing.

  • Objective 3
    Functional analysis of mutations in components of the stringent response in the switch between starvation and growth. The mutations include those discovered in evolved strains (objective 1 and 2), as well as those reported in the literature and random mutations (e.g. in relA). We will examine local effects of (p)ppGpp through allosteric interactions with enzymes or transcription factors, and global rearrangement of metabolism.