Difference between revisions of "Team:Korea U Seoul/Project/project overview"

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                   Project Overview
 
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    Sortases, enzymes that recognize and cleave the specific sorting signal of secreted proteins to form isopeptide bonds between the secreted proteins and polypeptides, function as protein ligase to form the cell-wall surface of gram-positive bacteria. In case of <i>C.diphtheriae</i>, which belongs to the same genus of our experimental bacteria <i>Corynebacterium glutamicum</i>, has total of 6 sortases, 5 pilus specific sortases (Srt A,B,C,D,E) and 1 housekeeping sortase (Srt F) involved in the formation of all types of pili. <br />
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  Synthetic biology researches are based on standardized biological parts, and the scientists should explore various metabolism databases to design their own devices or circuits. However, it is hard for researchers to design a proper biochemical pathway due to a considerable amount of data available on the Internet. Korea U Seoul, therefore, developed a web application ‘Gil’, which means “path” or “road” in Korean. This software is a spin-off version of ‘IPNN’ . A researcher can search which set of reactions or genes is required to conduct a successful experiment.
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There are 9 types of pillins that comprise pilus; Spa A, B, C, D, E, F, G, H, I, J. SrtA build up SpaA-type pili, which is composed of Spa A, B and C. Srt B/C and Srt d/E each forms SpaD-type pili and SpaH-type pili, which is made up of Spa D, E, F and Spa H, I, J respectively. Like this, the names of each pili types are generally from the names of many Spa proteins. <br />
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                          The software ‘Gil’ is a bio-pathfinder for synthetic biologists. Given only a reactant and a final product, a user can obtain possible paths using our program. For instance, if you want to break some agarose into pyruvate, the ‘Gil’ will show you maximum 12 optimal path composed of biologically proven reactions. In addition, the biological scoring system is another significant feather of this software.
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The picture below shows the process of SpaA type pili formation, using SrtA. Sortase class A enzymes recognize the sequence LPXTG at the carboxyl terminus of surface protein precursors. Cystein of SrtA recognizes LPXTG motif of SpaC, cleaves between T and G, forming SpaC-SrtA intermediate via nucleophilic attack. This intermediate is again attacked by lysine of SrtA bounded SpaA, and the process is continued to form SpaC–SpaAn–SrtA intermediates.<br />
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                          The ‘Gil’ is able to calculate the increase and decrease of the number of ATP, NADH, NADPH, and CO2, and provide the maximum three output paths, respectively. Also, the ‘Gil’ contains BioBrick part registry, E. Coli K-12 gene data, and the Gibbs free energy of each reaction. These information helps people find the most plausible de novo pathway just like Google Maps.
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Nucleophilic attack by Lysine of SrtF bounded SpaB form SpaC-SpaA(n)-SpaB-SrtF intermediate. The product of this SrtA reaction is covalently linked to lipidⅡ and is then incorporated into the cell wall envelope, terminating the formation of SpaA-type pilus.
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Revision as of 17:12, 18 September 2015

Project Overview

Synthetic biology researches are based on standardized biological parts, and the scientists should explore various metabolism databases to design their own devices or circuits. However, it is hard for researchers to design a proper biochemical pathway due to a considerable amount of data available on the Internet. Korea U Seoul, therefore, developed a web application ‘Gil’, which means “path” or “road” in Korean. This software is a spin-off version of ‘IPNN’ . A researcher can search which set of reactions or genes is required to conduct a successful experiment. The software ‘Gil’ is a bio-pathfinder for synthetic biologists. Given only a reactant and a final product, a user can obtain possible paths using our program. For instance, if you want to break some agarose into pyruvate, the ‘Gil’ will show you maximum 12 optimal path composed of biologically proven reactions. In addition, the biological scoring system is another significant feather of this software. The ‘Gil’ is able to calculate the increase and decrease of the number of ATP, NADH, NADPH, and CO2, and provide the maximum three output paths, respectively. Also, the ‘Gil’ contains BioBrick part registry, E. Coli K-12 gene data, and the Gibbs free energy of each reaction. These information helps people find the most plausible de novo pathway just like Google Maps.

(Architects at the bacterial surface — sortases and the assembly of pili with isopeptide bonds Antoni P. A. Hendrickx, Jonathan M. Budzik, So-Young Oh and Olaf Schneewind)

Description

The main objective of our project is to construct a novel “protein whip” platform, with which we can make Corynebacterium glutamicum to express other corynebacterium’s pili structure comprised of chains of a protein of our choice. As our first try, we decided to make pili made out of green fluorescence proteins (GFP); in order to do so, we substituted SpaA protein, one of the surface proteins in the Pilin A gene cluster, into green fluorescence protein, and transformed a vector containing the modified Pilin A gene cluster into a C. glutamicum strain.
Our “protein whip” platform is expected to have many practical applications. For example, pili made out of an enzyme, enzyme whip will enable the reaction to take place with high efficiency, for a great number of the enzyme included in the pili will be able to “attack” the reactants simultaneously. Biofilms made of strains of bacteria that express pili comprised of chains of specific amino acids such as histidine or cysteine that readily bind to heavy metals may be utilized to purify water contaminated with heavy metals.
Having a number of potential applications is not the sole merit of our project; by using C. glutamicum instead of widely exploited Escherichia coli, our project also contributes to expanding model organisms used in synthetic biology beyond E. coli.