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Team:Imperial College London/Project Chemotaxis Design
From 2011.igem.org
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<li><p>While malate-responsive sensors do not naturally occur in <i>E. coli</i>, they have been identified in several other bacteria species, including the soil microbes <i>Pseudomonas aeruginosa</i> PA01 strain & <i>Pseudomonas putida</i> KT2440 strain. PA2652 is a malate responsive chemoreceptor found in <i>P. aeruginosa</i> & mcpS is a receptor found in <i>P. putida</i> responding to a number of TCA cycle intermediates including malate<sup>[1][2]</sup>. The molecular mechanism of chemotaxis in <i>Pseudomonas aeruginosa</i> & <i>P. putida</i> are different to that of <i>E. coli</i>, however there is high degree of structural similarity between the proteins that make up the chemotaxis pathway. Since these proteins are structurally similar, it is reasonable to assume that the PA2652 or mcpS domain will interact with the native chemotaxis pathway in <i>E. coli</i> and the bacteria will be able to perform chemotactic response upon malate binding to an introduced receptor. </p></p> | <li><p>While malate-responsive sensors do not naturally occur in <i>E. coli</i>, they have been identified in several other bacteria species, including the soil microbes <i>Pseudomonas aeruginosa</i> PA01 strain & <i>Pseudomonas putida</i> KT2440 strain. PA2652 is a malate responsive chemoreceptor found in <i>P. aeruginosa</i> & mcpS is a receptor found in <i>P. putida</i> responding to a number of TCA cycle intermediates including malate<sup>[1][2]</sup>. The molecular mechanism of chemotaxis in <i>Pseudomonas aeruginosa</i> & <i>P. putida</i> are different to that of <i>E. coli</i>, however there is high degree of structural similarity between the proteins that make up the chemotaxis pathway. Since these proteins are structurally similar, it is reasonable to assume that the PA2652 or mcpS domain will interact with the native chemotaxis pathway in <i>E. coli</i> and the bacteria will be able to perform chemotactic response upon malate binding to an introduced receptor. </p></p> | ||
| - | < | + | <p><b>2. The construct must be as modular as possible.</p></b> |
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<li><p>Genetic constructs for expression of malate chemoreceptor are not complicated, however they are modular. Expression of the constructs is under constitutive expression of promoter J23100. It is provided from the registry in the biobrick K398500, in the backbone vector pSB1C3. The coding sequence has been removed from this construct using PCR, providing us with backbone vector with the constitutive promoter, to be assembled using Gibson or CPEC assembly. Ribosome binding sites (RBS) have been generated using Salis RBS calculator with relative translation initiation rates (TIR): 44050 & 42010 for mcpS and PA2652 respectively. The coding sequences for mcpS and for PA2652 have been codon optimised using our codon optimisation software, so that sequence is codon optimised for <i>E. coli</i>. We exploit terminator embedded in the backbone vector pSB1C3 for termination of transcription. In addition, modularity of our system is ensured by putting 15 bp insulator sequence between the RBS and the promoter. This sequence was specifically designed to make the promoter interchangeable without affecting the RBS strength and therefore translation initation rate is not affected by changing a different promoter in front of the insulator sequence. This allows us to change the promoter strength simply by changing promoter without modifying the whole genetic construct, thus it improves modularity of the construct. The insulator sequence acts as a starting point for PCR and it can be used to amplify the receptor sequence without the promoter.</p> | <li><p>Genetic constructs for expression of malate chemoreceptor are not complicated, however they are modular. Expression of the constructs is under constitutive expression of promoter J23100. It is provided from the registry in the biobrick K398500, in the backbone vector pSB1C3. The coding sequence has been removed from this construct using PCR, providing us with backbone vector with the constitutive promoter, to be assembled using Gibson or CPEC assembly. Ribosome binding sites (RBS) have been generated using Salis RBS calculator with relative translation initiation rates (TIR): 44050 & 42010 for mcpS and PA2652 respectively. The coding sequences for mcpS and for PA2652 have been codon optimised using our codon optimisation software, so that sequence is codon optimised for <i>E. coli</i>. We exploit terminator embedded in the backbone vector pSB1C3 for termination of transcription. In addition, modularity of our system is ensured by putting 15 bp insulator sequence between the RBS and the promoter. This sequence was specifically designed to make the promoter interchangeable without affecting the RBS strength and therefore translation initation rate is not affected by changing a different promoter in front of the insulator sequence. This allows us to change the promoter strength simply by changing promoter without modifying the whole genetic construct, thus it improves modularity of the construct. The insulator sequence acts as a starting point for PCR and it can be used to amplify the receptor sequence without the promoter.</p> | ||
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| - | <p><b> | + | <p><b>3. Uptake of bacteria into roots.</b> |
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<li><p>Root uptake of both <i>E. coli</i> and the bakers’s yeast <i>S. cerevisiae</i> can be observed in the model organism <i>Arabidopsis thaliana</i> and in tomato plants. It is a process that occurs naturally (althought it yet remains to be observed in soil) and we do not need to incorporate additional genes into our design.</p> | <li><p>Root uptake of both <i>E. coli</i> and the bakers’s yeast <i>S. cerevisiae</i> can be observed in the model organism <i>Arabidopsis thaliana</i> and in tomato plants. It is a process that occurs naturally (althought it yet remains to be observed in soil) and we do not need to incorporate additional genes into our design.</p> | ||
Revision as of 12:42, 21 September 2011
Module 1: Phyto-Route
Chemotaxis is the movement of bacteria based on attraction or repulsion of chemicals. Roots secrete a variety of compounds that E. coli are not attracted to naturally. Accordingly, we engineered a chemoreceptor into our chassis that can sense malate, a common root exudate, so that it can swim towards the root. Additionally, E. coli are actively taken up by plant roots, which will allow targeted IAA delivery into roots by our system.
Design
We aim to ensure that the specifications that were drawn up are considered in the design.
1. The bacteria should sense malate and actively move towards roots.
While malate-responsive sensors do not naturally occur in E. coli, they have been identified in several other bacteria species, including the soil microbes Pseudomonas aeruginosa PA01 strain & Pseudomonas putida KT2440 strain. PA2652 is a malate responsive chemoreceptor found in P. aeruginosa & mcpS is a receptor found in P. putida responding to a number of TCA cycle intermediates including malate[1][2]. The molecular mechanism of chemotaxis in Pseudomonas aeruginosa & P. putida are different to that of E. coli, however there is high degree of structural similarity between the proteins that make up the chemotaxis pathway. Since these proteins are structurally similar, it is reasonable to assume that the PA2652 or mcpS domain will interact with the native chemotaxis pathway in E. coli and the bacteria will be able to perform chemotactic response upon malate binding to an introduced receptor.
2. The construct must be as modular as possible.
Genetic constructs for expression of malate chemoreceptor are not complicated, however they are modular. Expression of the constructs is under constitutive expression of promoter J23100. It is provided from the registry in the biobrick K398500, in the backbone vector pSB1C3. The coding sequence has been removed from this construct using PCR, providing us with backbone vector with the constitutive promoter, to be assembled using Gibson or CPEC assembly. Ribosome binding sites (RBS) have been generated using Salis RBS calculator with relative translation initiation rates (TIR): 44050 & 42010 for mcpS and PA2652 respectively. The coding sequences for mcpS and for PA2652 have been codon optimised using our codon optimisation software, so that sequence is codon optimised for E. coli. We exploit terminator embedded in the backbone vector pSB1C3 for termination of transcription. In addition, modularity of our system is ensured by putting 15 bp insulator sequence between the RBS and the promoter. This sequence was specifically designed to make the promoter interchangeable without affecting the RBS strength and therefore translation initation rate is not affected by changing a different promoter in front of the insulator sequence. This allows us to change the promoter strength simply by changing promoter without modifying the whole genetic construct, thus it improves modularity of the construct. The insulator sequence acts as a starting point for PCR and it can be used to amplify the receptor sequence without the promoter.
3. Uptake of bacteria into roots.
Root uptake of both E. coli and the bakers’s yeast S. cerevisiae can be observed in the model organism Arabidopsis thaliana and in tomato plants. It is a process that occurs naturally (althought it yet remains to be observed in soil) and we do not need to incorporate additional genes into our design.
References
[1] Lacal, J., Alfonso, C., Liu, X. & et al. (2010) Identification of a chemoreceptor for tricarboxylic acid cycle intermediates: differential chemotactic response towards receptor ligands. Journal of Biological Chemistry, 285 (30), 23126 – 23136.
[2] Alvarez-Ortega, C. & Harwood, C. S. (2007) Identification of Malate Chemoreceptor in Pseudomonas aeruginosa by Screening for Chemotaxis Defects in an Energy Taxis-Deficient Mutant. Applied and Environmental Microbiology, 73 (23, 7793 - 7795.
Paungfoo-Lonhienne et al. (2010) Turning the table: plants consume microbes as a source of nutrients. PLoS ONE 5(7): e11915. http://www.nih.gov/science/models/arabidopsis/index.html
