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Team:IIT Madras/Project
From 2009.igem.org
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Synthetic biology is a new area of biological research that combines science and engineering in order to design and build ("synthesize") novel biological functions and systems. It involves plugging together existing genetic components in order to create new and unique systems. This application, titled the "Combinatorial Lock" introduces a new paradigm in gene regulation. The study is based on the concept of plasmid loss. Any episome introduced into the cell shows a segregational asymmetry accompanied with differential growth rates in the absence and presence of episome leading to an overall loss of the episomal unit in the absence of any maintaining selective pressure. It is hypothesized that by appropriately controlling the external selective pressures, we can thereby also control the direction of plasmid loss, modifying the existing gene regulation system in a pre determined manner. It is also hypothesized that introducing negative selective pressures against certain other directions of plasmid loss, in the form of constitutively repressed endotoxins will help streamline the regulatory system even further. If successful, this study allows for exquisitely delicate and precise multifactorial control of gene regulation in the future. It is expected that if successful, this model can be used to also hide genes of commercial interest to protect it from unauthorized use. |  |
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Summary
Our project is based on the fundamental concept of plasmid instability in a novel way to conceal information or ‘lock’ a gene’s function in a cell until the correct combination of inputs is fed into the cell. We call this a ‘combinatorial lock’. It involves the positive regulation of the gene of interest only on receiving the correct inputs from the user. We use plasmids which can confer resistance to certain antibiotics in the medium and link them up in a certain way (i.e, design a genetic circuit) so that they repress the expression of the gene of our interest. As the selection pressure is lifted from the media, the plasmids which have the repressors for the gene of interest are lost, hence revealing the gene on using the correct series of antibiotic washes. In essence, the process of unlocking would simply be the correct sequence of antibiotic media in which the cells should be washed. We would be working with both a 2 plasmid system as well as 3 plasmid system and it is easy to see that this principle, in theory, could be extended to n plasmids. We intend to demonstrate this with simulations in matlab. One can think of a number of potential applications of this system of ‘combinatorial locks’, an example being the field of medicine. Human body releases a myriad of chemicals everyday in a certain order according to external stimuli or otherwise. In case of a disease, if this order goes awry, then this lock can be used to release the required chemicals to bring back the desired equilibrium. Also, when one wants to have the expression of a gene of commercial interest available only to licensed users and not a third party, this lock could be used.
Theory
The most important idea behind the working of the lock is plasmid loss due to lack of selection. Any extra-chromosomal genetic material introduced into the cell tends to disappear over the generations, unless they confer a selective survival advantage over the cells that do not possess the plasmid. During the growth of bacteria, plasmid-free variants arise in the initially homogeneous plasmid-bearing cell population basically in two ways. First, each plasmid-bearing cell has a certain probability to give rise to a plasmid-free cell at cell division (this depends on the mechanisms of plasmid distribution between daughter cells, plasmid copy number at the cell division, the presence of multimer resolution loci, etc.). Usually, such probability is very low for natural plasmids (about 10-7) whereas recombinant plasmids (i.e. genetically modified) may segregate with a higher probability (10-3—10-5). Several hypotheses have been put forward to explain this tremendous difference: impaired copy number control, the absence/impairment of the multimer resolution genes and random distribution of plasmid among daughter cells for low copy number plasmids.
Second, it was experimentally found that plasmid-bearing cells usually have a lower maximum specific growth rate than their plasmid-free counterparts, and once a plasmid-free cell arises, it out-competes its plasmid-bearing counterparts very rapidly. Since most recombinant plasmids are not conjugative (not capable of self-transfer to other plasmid-free cells), if a cell has lost a plasmid, there is no way for the cell to acquire it again. Thus, a segregation of plasmids at cell division and the difference in the growth rates of plasmid-free and plasmid bearing subpopulations determine the rate at which plasmids are lost during prolonged cultivation. Here, we use plasmids which can confer resistance to certain antibiotics in the medium and link them up in a certain way so that they repress the expression of the gene of our interest. As the selection pressure is lifted from the media, the plasmids which have the repressors for the gene of interest are lost, hence revealing the gene on using the correct series of antibiotic washes.
Potential Applications
This has profound implications in the field of medicine in terms of regulated gene therapy and tissue specific control of drug release. The locking plasmid circuitry can be engineered to be incorporated into higher cells like our own. Such a system will detect the patterns of substances that are secreted by the cells and can activate a response if any link in a pathway has gone out of the way. This mechanism can also be used in bioreactors in industry, where certain functions of the bacteria are needed at specific stages of the fermentation. For instance, if a certain compound needs to be produced only after the culture reaches a predetermined population density, then the locking mechanism can be linked up a cell density related parameter for the timely secretion of the protein or a molecule of interest.
Work Plan
The cell will be transformed with 3-4 plasmids (depending on the length of code needed. It can be generalized to “n” plasmids). One of them will have the gene of interest which will be expressed only when all the plasmids apart from this particular one are lost in a particular order. This particular order or “code” will consist of a sequence of antibiotic treatments given to the transformed cells. The correct code triggers the loss of plasmids in the cells in a particular order. Each plasmid will be linked to the plasmids which are supposed to be lost before and after it in a very tightly regulated fashion. The regulation of the plasmid loss can be regulated very tightly using a “suicide gene” (gene coding for the bacterial gyrase poison). These genes will be triggered when the culture is subjected to the wrong antibiotic (Out of sequence). To ensure that the suicide genes don’t fire randomly, they are under the control of repressors which are on the plasmids that are supposed to be lost after it and are expressed constitutively. Thus, they fire only when the plasmid containing the repressor is lost. When all the plasmids other than the plasmid containing the gene of interest are lost, the repressors that have been blocking the required gene are lost, thus allowing its expression, which can manifest as a phenotype or a function in the cell. This will be the “unlocking” of the lock. As a proof of concept, we will not be using a gene of interest as such. Instead, we will make use of a fluorescent marker in each plasmid. After each antibiotic wash, the lost plasmid can be determined based on the absence of a specific fluorescent marker. This will tell us in what sequence the plasmid loss occurs and whether it matches with the theory proposed. Independently, we will be modeling the population growth dynamics due to sporadic and targeted loss of plasmids computationally. We will also be modeling the system to increase the number of digits in the code using the minimum number of elements in the plasmids. We plan to proceed with the experiment using a PCR based amplification system, followed by a specific restriction digest and subsequent ligation. The construction itself will proceed in a stepwise fashion, the details of which have not been elucidated in this section. Once the constructs are ready, they will be co-transformed into the appropriate strain of E coli, and the loss of plasmids will be monitored using the fluorescence from the reporter on each plasmid over a range of selective conditions varying with time.
