User:Jarle Pahr/Notebook/ppGpp Msc

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<!-- sibboleth --><div id="lncal1" style="border:0px;"><div style="display:none;" id="id">lncal1</div><div style="display:none;" id="dtext">02/03/2013,02/04/2013,02/05/2013,02/06/2013</div><div style="display:none;" id="page">User:Jarle Pahr/Notebook/ppGpp Msc</div><div style="display:none;" id="fmt">yyyy/MM/dd</div><div style="display:none;" id="css">OWWNB</div><div style="display:none;" id="month"></div><div style="display:none;" id="year"></div><div style="display:none;" id="readonly">Y</div></div>

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Project Description/Abstract

  • Msc. Thesis project to develop ppGpp fluorescent protein reporter system.


  • Rahmi Lale (
  • Eivind Almaas (
  • Martin F. Hohmann-Marriott (

Title Design of a gene circuit for monitoring bacterial stringent response on a single cell level.


Bacteria monitor changes in the environment and respond accordingly using an array of sensory systems. A recurring theme in such systems is the conversion of a stress signal into an increased concentration of a secondary messenger molecule which acts as a pleiotropic effector regulating the activity of numerous target enzymes (Pesavento and Hengge 2009).

One such system is the bacterial stringent response. This adaptation mechanism is mediated by the alarmone nucleotide guanosine pentaphosphate or tetraphosphate (ppGpp), which exerts its regulatory role by attenuating the activity of numerous enzymes, with RNA polymerase being the main target (Potrykus and Cashel 2008). The intracellular levels of ppGpp are controlled by the RelA-SpoT Homologue (RSH) family of proteins, which either synthesize or hydrolyze ppGpp in response to various stress stimuli (Atkinson, Tenson et al. 2011).

Current methods to detect the production levels of ppGpp molecule upon stress are laborious and involves techniques that are not suitable for single cell level measurements. Therefore in this project a gene circuit will be designed using promoters that are transcriptionally controlled by ppGpp to monitor cellular stringency. The gene circuit will also be modeled in order to have a quantitative understanding of how fluctuations in ppGpp levels affect stringent response using previously developed approaches (Ghim and Almaas 2008, 2009).

Relevant literature

Atkinson, G. C., T. Tenson, et al. (2011). "The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life." PLoS One 6(8): e23479.

Ghim, C. M. and E. Almaas (2008). "Genetic noise control via protein oligomerization." BMC Systems Biol 2.

Ghim, C. M. and E. Almaas (2009). "Two-Component Genetic Switch as a Synthetic Module with Tunable Stability." Physical Rev Let 103(2).

Pesavento, C. and R. Hengge (2009). "Bacterial nucleotide-based second messengers." Curr Opin Microbiol 12(2): 170-176.

Potrykus, K. and M. Cashel (2008). "(p)ppGpp: still magical?" Annu Rev Microbiol 62: 35-51.


RrnB GreA pellets.jpg


This project was completed in July 2013. Report available here: