Team:Edinburgh/logic/

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<h1>Bacterial Logic</h1>
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<p>This year Edinburgh’s team has looked at metabolic wiring – a new way for connecting logic gates in different cells. To understand how this works, and why it’s a big deal, first we have to look at bacterial computation.</p>
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<p>One of the most exciting developments in Synthetic Biology over the past decade has been the introduction of biological logic gates. For those who don’t know, logic gates are binary decision makers. They take in two signals, and emit a signal based on what signals are present. An AND gate, for example, will only emit a signal if it is receiving its two inputs. An OR gate will emit a signal if one of the two signals is present. And so on and so forth.</p>
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  <h1>Background</h1>
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<p>They have provided the foundations of all our computers for decades, and over the past decade, biological equivalents have been introduced into bacteria. They can be quite simple to understand – consider a pair of genes under inducible promoters. When they are both turned on, the protein products dimerise and act as a transcription factor for a third promoter. The system just described is a simple AND gate – the third gene product is the output, and it is only synthesised when the two inputs (which turned on the first two promoters) are present.</p>
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<p>So far so good. This is where the problems begin however.</p>
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<p style="font-style: italic;">In order to improve globally equality, both monetary and medically, the accessibility of new technologies is imperative. Our project designed a intercellular communication and control system that could be used to stabilise the composition of mixed populations of bacteria. This would simplify the use of complicated biological systems such as microbial consortia.</p>
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<p>To make complex decisions, you need multiple logic gates working in tandem, with the outputs of logic gates feeding directly into the inputs of others. However, you cannot simply make a super-intelligent bacterium by cramming it full of logic gates. There’s an upper limit to how many of these circuits a cell can hold before it starts having all sorts of issues – cross-talk begins to wear the system down, and sheer metabolic load makes the cells unviable. It just doesn’t work.</p>
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<p><em>But</em>, the reasoning went, hope is not lost. We can put the logic gates in <em>different</em> cells, and connect them with diffusible signals. Instead of an intelligent bacterium you would have an intelligent population of cells.</p>
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<p>Microbial consortia are populations of bacteria or other microorganisms that work together. They exist naturally and have been proven to be more robust and adaptable than monocultures<sup>1, 2</sup>. Why then do large scale biotech industries often use monocultures? The production of quorn<sup>3</sup> and antibiotics<sup>4</sup> are often done with only one species or strain of organism.</p>
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<p>This is a viable solution, and it’s the direction the field is moving in, but there are still problems. The systems that began to be built were wired up with quorum sensing molecules – not surprisingly, they’re designed for inter-cellular communication after all. But these are limited in number, which still imposes an upper limit on complexity. You also have an issue with turning off signals – if a signal is only meant to be on a for a short period of time, then it’s going to be a problem when the chemical signal remains in the medium long afterward.</p>
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<p>And so it was, that in 2013 a paper was published outlining a solution to all these woes. ‘Metabolic Wiring’ was the proposed solution.</p>
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<p>This is to prevent the effects of competition between strains. In environments where production of product can be detrimental to the organism’s health, adding in competition is adding another problem to the difficult task of optimizing production.</p>
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<p>In short, metabolic wiring replaces quorum sensing molecules with metabolites in a metabolic pathway. A cell that is to emit a signal, instead of secreting a quorum sensing molecule, produces an enzyme which performs the first step in a metabolic pathway. The compound now produced then diffuses out of the cell, into neighbouring cells, and when it comes into contact with cells with promoters sensitive to that signal (as part of a logic gate) the signal will have been propagated.</p>
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<p>The number of wires here is limited only by the number of metabolic pathways containing membrane diffusible compounds, and the great thing is that since the molecules are both signal and precursor for the next signal, the whole system is much more responsive – the signals quench themselves.</p>
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<p>Current uses of microbial consortia are subject to <a href="https://2014.igem.org/Team:Edinburgh/zeigler">problems</a>. These include: interspecies competition; sensitivity to changes in feedstock;  and long reestablishment times following reactor replacement. We attempt to solve these problems by introducing novel intercellular communication, greater responsiveness, and population control methods to our microbial system. These enable us to better regulate the composition of artificial microbial communities, while also allowing for more rapid feedback on its status, so that problems can be identified before the community collapses.</p>
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<p>And so, it is hoped, metabolic wiring should facilitate the development of much more intelligent systems. This could be the future of Bacterial Computation.</p>
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<p>If microbial consortia can be designed more easily, the possibility of using multiple strains of bacteria to produce complex biomaterials or degrade recalcitrant materials becomes ever more likely.<sup>5, 6</sup></p>
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<h3>References</h3>
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<ol><li>Wintermute, E. H., & Silver, P. A. (2010). Dynamics in the mixed microbial concourse. <em>Genes & Development</em>, 24(23), 2603-2614. doi: 10.1101/gad.1985210</li>
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<li>Sørensen, S. R., Ronen, Z., & Aamand, J. (2002). Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2. <em>Applied and Environmental Microbiology</em>, 68(7), 3478-3485. doi: 10.1128/aem.68.7.3478-3485.2002</li>
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<li>WIEBE, M. G., NOVÁKOVA, M., MILLER, L., BLAKEBROUGH, M. L., ROBSON, G. D., PUNT, P. J., & TRINCI, A. P. J. (1997). Protoplast production and transformation of morphological mutants of the Quorn® myco-protein fungus, Fusarium graminearum A3/5, using the hygromycin B resistance plasmid pAN7-1. <em>Mycological Research</em>, 101(07), 871-877. doi: doi:10.1017/S0953756296003425.</li>  
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<li>Hendlin, D., Stapley, E. O., Jackson, M., Wallick, H., Miller, A. K., Wolf, F. J., . . . Mochales, S. (1969). Phosphonomycin, a New Antibiotic Produced by Strains of Streptomyces. <em>Science</em>, 166(3901), 122-123. doi: 10.1126/science.166.3901.122</li>
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<li>Brenner, K., You, L., & Arnold, F. H. (2008). Engineering microbial consortia: a new frontier in synthetic biology. <em>Trends in Biotechnology</em>, 26(9), 483-489. doi: http://dx.doi.org/10.1016/j.tibtech.2008.05.004</li>
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<li>Rittmann, B. E., et al. (2006). A vista for microbial ecology and environmental biotechnology. <em>Environmental science & technology</em>, 40(4), 1096-1103.</li></ol>
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Latest revision as of 03:54, 18 October 2014

In order to improve globally equality, both monetary and medically, the accessibility of new technologies is imperative. Our project designed a intercellular communication and control system that could be used to stabilise the composition of mixed populations of bacteria. This would simplify the use of complicated biological systems such as microbial consortia.

Microbial consortia are populations of bacteria or other microorganisms that work together. They exist naturally and have been proven to be more robust and adaptable than monocultures1, 2. Why then do large scale biotech industries often use monocultures? The production of quorn3 and antibiotics4 are often done with only one species or strain of organism.

This is to prevent the effects of competition between strains. In environments where production of product can be detrimental to the organism’s health, adding in competition is adding another problem to the difficult task of optimizing production.

Current uses of microbial consortia are subject to problems. These include: interspecies competition; sensitivity to changes in feedstock; and long reestablishment times following reactor replacement. We attempt to solve these problems by introducing novel intercellular communication, greater responsiveness, and population control methods to our microbial system. These enable us to better regulate the composition of artificial microbial communities, while also allowing for more rapid feedback on its status, so that problems can be identified before the community collapses.

If microbial consortia can be designed more easily, the possibility of using multiple strains of bacteria to produce complex biomaterials or degrade recalcitrant materials becomes ever more likely.5, 6


References

  1. Wintermute, E. H., & Silver, P. A. (2010). Dynamics in the mixed microbial concourse. Genes & Development, 24(23), 2603-2614. doi: 10.1101/gad.1985210
  2. Sørensen, S. R., Ronen, Z., & Aamand, J. (2002). Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2. Applied and Environmental Microbiology, 68(7), 3478-3485. doi: 10.1128/aem.68.7.3478-3485.2002
  3. WIEBE, M. G., NOVÁKOVA, M., MILLER, L., BLAKEBROUGH, M. L., ROBSON, G. D., PUNT, P. J., & TRINCI, A. P. J. (1997). Protoplast production and transformation of morphological mutants of the Quorn® myco-protein fungus, Fusarium graminearum A3/5, using the hygromycin B resistance plasmid pAN7-1. Mycological Research, 101(07), 871-877. doi: doi:10.1017/S0953756296003425.
  4. Hendlin, D., Stapley, E. O., Jackson, M., Wallick, H., Miller, A. K., Wolf, F. J., . . . Mochales, S. (1969). Phosphonomycin, a New Antibiotic Produced by Strains of Streptomyces. Science, 166(3901), 122-123. doi: 10.1126/science.166.3901.122
  5. Brenner, K., You, L., & Arnold, F. H. (2008). Engineering microbial consortia: a new frontier in synthetic biology. Trends in Biotechnology, 26(9), 483-489. doi: http://dx.doi.org/10.1016/j.tibtech.2008.05.004
  6. Rittmann, B. E., et al. (2006). A vista for microbial ecology and environmental biotechnology. Environmental science & technology, 40(4), 1096-1103.



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