Debunking myths on genetics and DNA

Sunday, September 15, 2013

Bacteria to the rescue!

Last month I talked about a cancer killing virus. Well, guess what comes next? A cancer killing bacterium, of course! :-) Our hero is once again, the one and only E. coli, a bacteria that normally resides in our guts and that is much beloved by experimentalists because it's cheap and easy to grow.

In 2011, a group from Nanyang Technological University, in Singapore, genetically modified a strain of E. coli so it would sense and kill the human pathogen Pseudomonas aeruginosa[1], a bacterium responsible for infections that can be lethal in immunochallenged subjects. Pseudomonas aeruginosa is resistant to many currently available antibiotics. On the other hand, therapies that do succeed in killing the bacterium also kill other bacteria that are part of a healthy microbiome.

How to eradicate a Pseudomonas aeruginosa infection without harming the "good" bacteria, then?

When in highly competitive environments, bacteria produce toxins, called bacteriocins, that kill closely related, competing strains. The bacteriocin that Pseudomonas aeruginosa produces is a toxic peptide called pyocin. The advantage of using such toxins instead of antibiotics is that, while resistance to antibiotics appears relatively early after therapy thanks to lateral transfer, no toxin-resistant strains have been observed so far.
"Given the stalled development of new antibiotics and the increasing emergence of multidrug-resistant pathogens, using synthetic biology to design new treatment regimens for infectious disease could address an urgent need [1]."
So, how does the bioengineered E. coli kill the pathogens? In order to "communicate" with one another, bacteria release a number of chemicals whose concentrations are proportional to the population density. These exchanges are called "intercellular quorum communication", or quorum sensing, and enable bacteria to turn "on" or "off" gene expression depending on the surrounding cell density of the population (i.e. when the concentration of molecules signaling a certain status reach a specific threshold). One of such mechanisms regulates the production of pyocin. Saeidi et al. [1] reproduced this regulatory mechanisms to enable their bioengineered E. coli to "sense" the presence of Pseudomonas aeruginosa, release the toxin, and kill it.
"Upon reaching a threshold concentration, the lysis E7 protein perforates membrane of the E. coli host and releases the accumulated pyocin S5. Pyocin S5, which is a soluble protein, then diffuses toward the target pathogen and damages its cellular integrity, thereby killing it [1]."
But wait, what about cancer? Eradicating cancer faces similar issues: you need to kill all the "sick" cells without harming the healthy ones. Chemotherapy drugs often end up damaging healthy cells too, hence the need of "targeted" drugs, drugs that can be delivered exclusively to the cancer cells.

A group from the University of Maryland used the quorum sensing mechanisms intrinsic in the bacterium to make it sense cancer cells. And while it doesn't quite kill the cancer cells, this research is important because the bacterium could become a means to transport specific drugs to the cancer tissues, while leaving the healthy cells untouched.
"By altering their quorum sensing genetic circuits, we engineered bacteria to find cells of interest (diseased or otherwise), dock on associated surface receptors or biomarkers (‘features’), integrate surface feature density, and also decide whether or not to initiate gene expression. This ‘smart’ bacterium reinforces the notion of an expanded synthetic biology umbrella that confers new capabilities on the individual cell. The resultant cell has capabilities that could be viewed as analogous to a dirigible—a transport vehicle that autonomously navigates and carries or deploys important cargo [2]."
The principle is the following: 1. find a biomarker that can "flag" the target cell and distinguish them from the healthy cells; 2. using the biomarkers as flags, deploy "nanofactories" to the target cell and have them produce the "quorum sensing" chemicals; 3. once quorum sensing is triggered, the bioengineered E. coli "swim" to the target cells.

Nanofactories are made of an antibody motif for binding to the cell and a fusion protein that produces quorum molecules when bound to the targeted bacterium [3]. In [2], Wu et al. used squamous cancer cells of the head and neck as target cells. These express EGFR, epidermal growth factor receptor, at a high threshold, which was used as biomarker. The nanofactories bound to EGFR and synthesized AI-2, the quorum sensing molecule that stimulated E. coli motility.
"In summary, the docking of anti-EGFR-NF onto mammalian cell surfaces was specifically controlled by EGFR surface density which, in turn, controlled subsequent AI-2 synthesis, bacteria migration, and the switching response phenotype. The signal generating and cell recruiting design shown here provides a tractable means to ensure site-specific gene initiation, providing a focused and predicted phenotype."
In the future, the cancer-sensing E. coli could become an efficient transporter of drugs aimed at destroying cancer cells while leaving the healthy cells intact.

[1] Nazanin Saeidi, Choon Kit Wong, Tat-Ming Lo, Hung Xuan Nguyen, Hua Ling, Susanna Su Jan Leong, Chueh Loo Poh & Matthew Wook Chang (2011). Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen Molecular Systems Biology DOI: 10.1038/msb.2011.55

[2] Hsuan-Chen Wu, Chen-Yu Tsao, David N Quan, Yi Cheng, Matthew D Servinsky, Karen K Carter, Kathleen J Jee, Jessica L Terrell, Amin Zargar, Gary W Rubloff, Gregory F Payne, James J Valdes & William E Bentley (2013). Autonomous bacterial localization and gene expression based on nearby cell receptor density Molecular Systems Biology DOI: 10.1038/msb.2012.71

[3] Rohan Fernandes, Varnika Roy, Hsuan-Chen Wu & William E. Bentley (2010). Engineered biological nanofactories trigger quorum sensing response in targeted bacteria nature nanotechnology DOI: 10.1038/nnano.2009.457


  1. Using bacteria and viruses to combat various conditions seems to be getting a lot of good momentum. This is great. Essentially, we are reusing pre-built nano-machines rather than having to build our own from scratch.

    On a different topic but related to your nice picture at the header, have you seen this:

    1. I hadn't seen those, beautiful! the most impressive flower explosion I've seen is this:


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