CHE.496/2009/Schedule/Oral presentations of part design/Group 4

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CHE.496: Biological Systems Design Seminar


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Group 4

  • Members: Dan Tarjan & George Washington


  • Antibodies
    • Giving engineered cells the ability to specifically detect and/or attach to many different types of targets has many applications. Abs are known for a variety of ligands. Their properties have also been studied and characterized extensively, which would support their integration into a rationally designed framework.
  • Sensor signal transduction mechanisms
    • Complex engineered biological systems may require many sensors to carry out their functions. Expanding the number of messengers and other mechanisms available to transduce these signals would support increased environmental awareness by these systems as well as responsiveness to the same.
  • Cell cycle responsive promoters

Stress responsive promoter


This promoter would be able to turn on/off genes in response to the stringent response mechanism in bacteria.


ppGpp(p) is an alarmone which gets produced in response to low levels of amino acids in the cell. Having a promoter responsive to this cellular signal would allow an engineered response certain types of stress on the cell. An example would be to put your synthetic metabolic network under control of a promoter that either gets directly inhibited by this signal or alternately, have such a promoter cause the production of an inhibitor for your synthetic genes.


ppGpp is produced by RelA and SpoT [1]. RelA is associated with ribosomes and is activated when an uncharged tRNA is in the A position. The precise triggers for SpoT is not known but it is activated in response to nutrient limitations including carbon starvation. ppGpp binds to RNA pol. and affects its translational targeting. It represses rRNA synthesis and also activates the rpoS gene, which codes for σ38. Promoters responsive to this RNAP/σ38 could be activated in response to stress/starvation. DksA, a ppGpp co-regulator, further regulators several promoters in response to stress. [2]

Taking advantage of these cellular handles to have a feedback signal for an engineered metabolic network is useful, however these signals have many natural functions which may complicate their use as regulators. [3] Further, these promoters may be responsive to additional regulation that is useful for their natural use but may be undesirable in an engineered system.


The following promoters are known to be either positively or negatively regulated due to the stringent response:

  • rrn -rRNA promoter- (repressed) GenBank: J01694.1
  • uspA -universal stress protein A promoter- (induced)
  • livJ -amino acid transport facilitating protein- (induced)

Source & References

  1. Magnusson et al. (2005) Trends in Microbiology 13, 236 [Magnusson-2005]
  2. Magnusson LU, Gummesson B, Joksimović P, Farewell A, and Nyström T. Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli. J Bacteriol. 2007 Jul;189(14):5193-202. DOI:10.1128/JB.00330-07 | PubMed ID:17496080 | HubMed [Magnusson-2007]
  3. Jishage M, Kvint K, Shingler V, and Nyström T. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev. 2002 May 15;16(10):1260-70. DOI:10.1101/gad.227902 | PubMed ID:12023304 | HubMed [Jishage]
All Medline abstracts: PubMed | HubMed

Part 6