Jul 2, 2011

iGEM - Grand Prize 2009 - Biosensors and Synthetic Biology.

by Bio! Mexico 
A classical biosensor consists in two main parts: a biological system -e.g. cells, nucleic acids membrane receptors or tissue fragments- which responds to a particular stimulus, and a transduction system, which transforms this biological response into an electrical output. This signal can then be adjusted to a defined scale, so it is possible to acquire quantitative information about the initial stimulus.

The specificity of biological molecules opens to biosensor a wide application spectrum in biomedical and industrial areas. Nevertheless, their calibration remains technically demanding.

Among the most successful biosensor applications are the glucose biosensors based on the activity of the enzyme Glucose Oxidase. This mechanisms are used for the daily monitoring and control of glucose levels in diabetes patients, representing a significant improvement for their life quality because it is known that the progression of diabetic complications is tightly related to the control of the patient glycemic levels.

The are also advances in biosensors for the industrial and enviromental areas. For example, luminiscent responses have been adapted to be arised by different stimuli in living cells. Among the stimuli that can be detected are pollutants like toluene, trichloroethylene, napthalene, salicilates, polychlorinated biphenyls, phenols and heavy metals. The biosensor's response time exhibit a notorious dependence on the biosensor's detection limit, thus, in order to detect low pollutant quantities, the biosensor needs more time to respond. This response time is between a range of 8 minute (for napthalene) to 15 h (for mercury), with detection limits that span from 27.2 ng/L (for the mentioned 15 h mercury biosensor) to  1.5 mg/L (for polychlorinated byphenils).

It is clear that not all biosensor have response time and detection limits suitable for their application for in-line monitoring at industrial level, as the detection of very low pollutant concentrations is needed. Nevertheless, biosensor have a valuable advantage compared with common chemical detection methods, and it is that biosensor are ecologically amenable. Furthermore, the fact that biosensor's detection limit may be not in the adequate range doesn't make biosensor lose their value, as long as they are still useful for pollutant early detection and for mixtures detection.

The main challenge for environmental and industrial biosenors is to lower their detection limit and increase the robustness. And this is a good challenge for Synthetic Biology to accept.

At iGEM, projects centered on biosensors or which at least involve a quorum sensing module, are quite popular. But among these projects, the work of the 2009 Cambridge University team is one of those which deserve a special mention.

In their project, the Cambridge students made two main contributions: a sensitivity tuner system and a set of reporter pigments. Their effort was rewarded with the 2009 iGEM Grand Prize.

The sensitivity tuner system is based on a previous work, also by Cambridge students but from the year 2007. This mechanism is a signal amplifier and consists on a stimuli receptor that responds producing an activator, which in turn produces a more powerful transcriptional response. In this way, it is possible that a very subtle stimulus may elicit a detectable transcriptional response, detectable by a reporter gene.

Sounds familiar? Of course! This means a possible solution for the biosensor's detection limit challenge. The 2009 Cambridge team  performed the task of quantitatively characterizing the magnitude of the signal amplification for twelve sensitivity tuner constructions.The British team also adapted the biosynthetic pathway of three visible pigments: carotenoids (orange/red), melanin (brown) and violacein (purple/green). 

Up: black box diagram of the sensitivity tuner 
and the pigment generator. Down: detailed diagram of the
same systems.
But the Cambdrige team went further. They designed and proposed a system of submersible strips based on their pigment production and sensitivity tuner systems. Attached to these strips in discrete dots would be present different strains of biosensor microorganisms ordered according to their detection limit. Thus, when a strip is submerged in a solution where substance "X" is present, the dots will produce visible pigment depending on the substance concentration, starting with the more sensible strains (which response to minimum amounts of stimulus) and ending with the less sensible strains (which need more stimulus to elicit a response). 

The dotted strips.
In conclusion, the Cambridge 2009 team made an important and original contribution for the biosensor's adaptation to industrial requirements, everything in a way that would be perhaps inconceivable without Synthetic Biology tools.  For sure, the biosensors area was not the same after iGEM 2009.

List of iGEM teams which have worked with biosensor or quorum sensing until 2008:

  • 2007 Brown UniversityLead sensor/Tristable switch
  • 2007 Colombia
    Iron sensor
  • 2007 Freiburg
    Protein Ca sensors/Protein light sensors
  • 2007 Glasgow 
    Toluene sensing and electric signal emission
  • 2007 Imperial College
    Biofilm sensor of AHLs/Temperature sensor for meet
  • 2007 Melbourne
    Light sensing E. coli with agregation and gas vesicle module
  • 2007 Mississippi StateUbiquitin ligase activity assay
  • 2007 MIT              
    Mercury biosensor
  • 2007 Naples   Oleic acid biosensor for determining olive oil purity
  • 2007 NYMU Taipei    
    Mammalian insulin secretor with glucose sensing module
  • 2007 Prairie View      
    Metal and organic compound biosensor
  • 2007 Saint Pettesburg  Copper biosensor with Schmitt trigger
  • 2007 Southern Utah  Cyanide biosensor in Pseudomonas fluorescens
  • 2008 Brown University  Electricic signal producer-arsenic biosensor
  • 2008 Harvard            
    Electrical signal output by Shewanella oneidensis to enviromental input
  • 2008 Illinois    G Protein  receptor coupling to pathogenous-associated-antigen-specific antibody and GFP downstream coupling/tyrosine kinase receptor   coupling to pathogenous-associated-antigen-specific antibody and GFP downstream coupling/GFP fragmentation and binding to antibodies directed to specific multiantigens, where they would complement and fluoresce, in Yeast.
  • 2008 Imperial College  Light sensing B. subtilis biomaterial pattern generator through motility arrest
  • 2008 Johns Hopkins  Yeast mate-type biosensor
  • 2008 Missouri Miners   Ethanol and methanol sensor with AOX promoter coupled to GFP
  • 2008 Newcastle U.   B. subtilis that detects pathogenic organisms by their quorum sensing mechanisms, and emits fluorescent signal
  • 2008 NTU Singapore   
    Quorum sensing bacteria which also respond with colicin secretion
  • 2008 Prairie View      
    Cation biosensor, which emits positive signal when cations are present, and negative when anions are.
  • 2008 Purdue      Biosensor for UV radiation, combining the SOS pathway promoter with a lacZ gene.
  • 2008 TU Delft   Temperature sensing E. coli through a RNA effector
  • 2008 U. of Alberta      
     biosensor/plant biobricks/butanol synthesis
  • 2008 U. of Sheffield   
    E. coli biosensor of V. cholerae through quorum sensing
  • 2008 Utha State    
    E. coli PHB biosensor that would aid in monitoring the PHB production in culture
  • 2009 Brown            
    Hystamine biosensor in Staphylococcus epidermidis chassis
  • 2009 Cambridge        
    Biosensor with input sensitivity tuner module and three different colour output depending on input strength/ biobricks for six pathways for different coloured outputs
  • 2007 Missouri           
     Biological timer and an ethanol Yeast biosensor
  • 2007 Penn State    
    Xylose metabolism modification/Radiation biosensor
  • 2007 Valencia           
    Promoter biosensor callibrator
  • 2008 BCCS Bristol   
    Structure and material organizationby bacteria, using chemotaxis, enviromental sensing and cell-cell communication
  • 2008 Beijing            
     Polychlorinated biphenyls- and -dioxins sensing and degrading E. coli
  • 2008 Caltech          
    Quorum sensing of pathogenic population by a strain of E. coli capable of oxidative burst/b-galactosidase secreting E. coli in the gut for lactose intolerance/folate secreting E. coli/ Multipotent E. coli
  • 2008 Turkey            
    Metal sensing and carrying E. coli
  • 2008 UNAM-IPN      
    Horizontal gene transfer sensor/turing pattern generator circuit
  • 2009 Br. Columbia    
    Module that receives input and transform it on a signal that varies according to input concentration from green to red output
  • 2007 Turkey        
    Tricolor pulse oscilator/subpopulation differentiation and competing mechanism/metal bacterial intake and taxis
  • 2008 Heidelberg
    E. coli biosensor and chemotaxis directed to pathogenic organisms through quorum sensing mechanism, and bacteriocidal production through another quorum sensing mechanism
  • 2008 NYMU Taipei  
    E. coli intented to attach and sense pH in the small-intestine and respond with removal of urea and guanidine, and also regulate phosphate balance.
  • 2008 Tokyo Tech   
    Low-pressure biosensor
  • 2008     U. of Lethbridge  PCB 
    E. coli biosensor with chemotactic and degradation modules. Also, riboswitch and SELEX

Jul 1, 2011

iGEM - Grand Prize 2010 - Metabolic Engineering and Synthetic Biology: DNA scaffolds for biochemical pathway improvement.

by Bio! Mexico 

Cell signaling pathways and cascades are  classic textbook topics which I discovered in my high school days and which fascinates me ever since, just as it does to any student who (truly) begins his journey into the marvelous realm of Molecular Biology.

Back then, me and my friends -at the Biology Olympiad preparation in Mexico City- use to compete to see who knew best the different kinds of G proteins, the cell responses and the evolutionary conservation of the MAP kinases pathway. I remember very well the morning when one of my friends came to us for breakfast, with the look of someone who spent the whole night reading meticulously, and introduced us to the JAK-STATs with such an enthusiasm that it was midnight when we were done reading and speculating... something that was a sort of a sport for us.

One of those afternoons, I started reading with more detail about a certain kind of proteins: the scaffold proteins. These proteins carry the function of binding to different kinases -or another kind of signaling protein- through their binding domains, so these kinases could be near each other. This spatial localization of interacting proteins facilitates signal transmission. In a word, these scaffold protein bring together interacting signaling proteins to boost the signal transmission.

The years went by, and one day it reached my ears the rumor that an iGEM was being organized in our school -the UANL Biological Sciences School- so we immediately started organizing meetings, in order to generate ideas and a project.

One of these ideas -a product of the oh, so many cups of coffee I drank and the long lonely hours I spent scribbling here and there- consisted on building chimeric enzymes which carried a binding domain, in such a way that when a designed protein scaffold was expressed, those chimeric enzymes would bind to it and come into proximity. If the enzyme used were part of a biochemical pathway, then, this pathway yield would be enhanced.

Among the contributions I claimed the project would make were: the fact that the yield of a biochemical pathway could be enhanced, the possibility of controlling the pathway's efficiency through the control of the scaffold's expression, and finally, the possibility of re-routing biochemical pathways through the inclusion of the enzymes responsible of the critical steps.

I cannot describe the surprise I felt when I stumbled upon a publication by Dr. John Dueber, which was entitled: Synthetic protein scaffolds provide modular control over metabolic flux . The authors commented how, using scaffold proteins, they were able to regulate the flux through the mevalonate and the glucaric acid pathways. They presented data about reduction of metabolic strees inside the cells and also pointed that these proceeding could be generalized for other metabolic pathways and that it represented an additional regulation level of protein expression. My ethical sense forced me to present to my team partners the work of Dr. Duebe, along with another interesting data published by Dr. Caleb Bashor.

In spite of my initial enthusiasm and the feeling of having hit with an idea without precedents, I soon noticed that what the idea had of original was the only fact that we would be implementing the scaffold system in BioBrick format. So I started again thinking and wondering -with coffee in hand and my eyes circles in bloom- on how could I improve this scaffold idea... Then, news came from the Massachusetts.

Scheme of a DNA scaffold.
The students from the Ljubljana University had just won the BioBrick Grand Prize after having developed a fabulous solution: instead of using proteinic scaffolds, they designed DNA scaffolds!

Uh, DNA scaffolds, but how do they work? Well, let's recall from the Cell Biology clasess that the are proteins which have peptidic domains that bind to certain DNA sequences. This DNA-binding domains have been widely used in other applications, like yeast two-hybrid assays, but the Ljubljana 2010 iGEM team had found another extraordinary application: use them to build chimeric enzymes, so that these chimerical construction can bind to DNA in an ordered fashion. In such a way, the enzymes of a pathway could be put near each other just like with protein scaffolds! 

Note that this enzyme recruitment is possible because there is no such thing as a nuclear membrane in bacteria, so DNA is accessible for binding proteins.

Violacein yield as registered when using
an ordered DNA scaffold program (green), 
a scrambled program (red), and a random program 
(purple) as negative control.
Furthermore, the Slovenian team not only made the biosynthesis of violacein and carotenoids more efficient, but they also found that this efficiency increase was more pronounced when the DNA program -i.e. the order of the recognition nucleotide sequence- matched the order of the biochemical pathway. They also explored possible application of DNA scaffolds in the refinement of synthetic genetic circuits, like oscillators.

This huge advanced for Synthetic Biology was presented under the title: "DNA coding beyond triplets" and it is perhaps just a matter of time until we see new results and new applications for this system. And, well... obviously, my iGEM team (UANL_Mexico 2011) then decided to work with something different!