Team:TU Delft-Leiden/Human Practices/Biosensors

Microbial Biosensors

A biosensor is a analytical device which makes use of a biological component to detect an analyte [1]. This biological component is broadly defined and could include enzymes, nucleic acids, and antibodies. Here, we will focus on whole cell microbial biosensors. In whole cell biosensors, the biological component consists of a living cell [2]. The use of whole cell microbial biosensors has certain advantages over the use of other biosensors and non-biological sensors.

One of the major advantages of whole cell biosensors is that they are able to detect substances by class, and not only one specific substance [3]. Another advantage is that microbial biosensors can give not only analytical output (ie. what is the concentration of the analyte?) but also functional output (ie. how does my living system respond to the analyte?) [2]. In our discussion with Mr. Van Der Burg of BioDetection Systems [ref to interview], he mentioned in this context that with their whole cell biosensors, they stay close to the physiology of the subject to exploit this.

The biggest advantage of microbial biosensors however is the fact that evolution has already created an enormous amount of biosensors for us. Organisms sense environmental compounds to influence their decisions; they will only make a certain metabolic enzyme if the specific metabolite is sensed. Evolution has optimized such systems, thus creating bioreceptors for a lot of compounds [4]. This is used to find to find “new” biosensors: Mr Van Der Burg [ref to interview] has told us that to find a dioxin bioreceptor, they “[search] for dioxin receptors which might have arisen in species living in contaminated areas.”

The most used sensing elements are promoter regions involved in the response of the cell to the target chemical. [3] With synthetic biology techniques, it is possible to isolate and enhance this promoter region and connect them to the appropriate reporter system. Currently, the most used reporters are genes which yield an optical (colorimetric, fluorescent, bioluminescent) signal. [3] These signals are processed with the use of various microscopy set-ups.

As already mentioned, nature has provided with a large array of possible microbial biosensors. With this as a start, a lot of whole cell biosensors have been developed. This is illustrated by the fact that only in iGEM, hundreds of biosensors have been developed. Also, D’Souza [4] published a list of 44 papers describing biosensors already in 2001. However, microbial biosensors have only very limitedly been commercialized. Su et al. [5] state: “Commercial microbial biosensors are just tips of the iceberg compared to the great amount of academic research on them”. They relate this to “the intrinsic disadvantages (slow response, low sensitivity, and poor selectivity)” of microbial biosensors, which, however, can and will be solved by the developments in synthetic biology [5].

One major reason microbial biosensors are currently limitedly used is not mentioned by Su et al., namely the fact that most current microbial biosensors require a microscopy set-up to be read out, due to the optical nature of their output. “For light and fluorescence assays you need lots of equipment and devious procedures,” Mr. Van Der Berg of BDS has explained to us [ref to interview]. The equipment mentioned is very expensive: For instance, even the Zephyr DIY fluorescence microscope developed by iGEM team TU Delft 2013 costs around $1500, and this is already extremely cheap compared to commercially available machines. [6]

The need for bulky microscopy equipment and complicated procedures currently limits the use of whole cell biosensors to advanced laboratories with highly trained personnel. This greatly reduces the possibility for commercially viable applications. Whole cell biosensor-based consumer products are under the current circumstances impossible, but also business-to-business products would only be available for the small subset of companies which has (or can afford to pay for) a lab and technicians.

To higher the chances for commercial applications of microbial biosensors, outputs other than light-based outputs are needed. Several other output mechanisms are available. Bousse [2] mentions multiple methods to measure the energy metabolism of cells (including pH measurement and measurement of oxygen consumption). All these measurement require that the analyte has a distinct influence on the metabolism of the cell, for example due to toxicity or increased cell growth. This greatly limits the range of analytes which can be tested and also makes the construction of new sensors with synthetic biology techniques very difficult. Several other methods based on changing pH or redox potential have been described [7]. However, these methods are not widely used and much less popular than light-based outputs.

From these observations, it can be concluded that, in order to make a commercial application of a microbial biosensor possible, a novel output mechanism has to be developed. The novel output has to meet several requirements. Firstly, its output signal should be measurable with the use of equipment which is inexpensive, portable, and easy to handle by non-specialists. Secondly, the signal should be easily quantifiable: the relation between analyte concentration and output signal should be smooth [denk na over formulering, dit is misschien te wiskundig]. Thirdly, the output system should be modular. This means that different sensing elements (for example promoters) should be easy to connect to the output mechanism. Stated in a different way, the biosensor should have plug-and-play functionality.

References

[1] Turner, Anthony; Wilson, George and Kaube, Isao (eds.) (1987). Biosensors:Fundamentals and Applications. Oxford, UK: Oxford University Press. p. 770

[2] L .Bousse, “Whole cell biosensors”, Sensors and Actuators B34 (1996) 270-275

[3] T. Vo-Dihn, B. Cullum, “Biosensors and biochips: advances in biological and medical diagnostics”, Fresenius J Anal Chem (2000) 366 :540–551

[4] S.F. D’Souza, “Microbial Biosensors” Biosensors & Bioelectronics 16 (2001) 337–353

[5] L. Su, Y. Lei, et al. “Microbial biosensors: A review” Biosensors and Bioelectronics 26 (2011) 1788–1799

[6] https://2013.igem.org/Team:TU-Delft/Zephyr (accessed on 30-9-2014)

[7] French CE, de Mora K, Joshi N, et al. “Synthetic biology and the art of biosensor design”. In: Institute of Medicine (US) Forum on Microbial Threats. The Science and Applications of Synthetic and Systems Biology: Workshop Summary. Washington (DC): National Academies Press (US); 2011. A5. Available from: http://www.ncbi.nlm.nih.gov/books/NBK84465/