Team:UiOslo Norway/Project

From 2014.igem.org

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<h3>Organ</h3>
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<h2>Our Project - The microOrganizer</h2>
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<p>The cell is the basic structural, functional, and biological unit of all known living organisms. Because the cells have all equipment and expertise necessary to carry out the functions of the life, they are considered the smallest unit of life that can replicate independently.</p>
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<p>The aim of our project was to build a system for physically connecting different bacteria in a predetermined manner. Throughout the iGEM competition we have designed surface markers that enable bacteria to bind to each other and to respond to the binding by a mechanism that would allow us to select for bound bacteria. A succesful system would allow us to organize different types of bacteria in a culture and we have therefor named our project «The microOrganizer».</p>
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<p>The unicellular organisms are made up with just one cell and their main groups are: bacteria, archaea, protozoa, unicellular algae and unicellular fungi.</p>
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<p>On the other hand the multicellular organisms are more complex and consist of multiple cells. The animals, including human beings, are multi-cellular. An adult human body is composed of about 100,000,000,000,000 cells!</p>
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<p>Each cell has basic requirements to sustain it, and the body's organ systems are largely built around providing the many trillions of cells with those basic needs (such as oxygen, food, and waste removal).</p>
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<p>A tissue, such as muscle, nervous and connective tissues, is an organized system composed with different kinds of specialized cells.</p>
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<p>Similarly, an organ is an organized and differentiated structure of various tissues performing independently a specific function, such as the stomach, the skin and the brain.</p>
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<p>The organs carry out functions as:</p>
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<li>Communication between cells</li>
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<li>Supplying the cells with nutrients</li>
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<li>Controlling exchanges with the environment</li>
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<p>Source: <a href="http://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/15625600 8/09/2011">http://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/15625600 8/09/2011</a></p>
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<h3>Microorganism</h3>
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<h2>The Parts</h2>
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<p>A microorganism or microbe is a diverse unicellular or multicellular mostly microscopic organism that includes all the bacteria and archaea and almost all the protozoa. They have also some members of the fungi, algae, and animals.</p>
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<h3>Split Enzyme Principle</h3>
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<p>They are considered the oldest form of life on Earth and wandered it hundreds of millions of years before the dinosaurs.</p>
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<p>A split enzyme is an enzyme split into two or more non-functional parts with intact tertiary structure. This means that the enzyme can be active if the different parts come together and assemble into the original enzyme. The enzyme parts have a natural affinity for each other and can assemble spontanously. We wanted to expose two different parts of a split enzyme on the surface of different bacteria.</p>
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<p>Microorganisms can be found and are able to live in every part of the biosphere including terrestrial, aquatic and extraterrestrial habitats, extreme environments and in other organisms, such as our digestive systems. Similarly, they are tolerant to many different conditions such as limited water accessibility, high salt content and low oxygen levels. Although they are well adapted, not every microorganism can survive in all habitats, as each type of it has developed to live within a narrow range of conditions.</p>
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<p>These organisms are essential components of every ecosystem. Indeed, they are essential to nutrient recycling and other compounds throughout the environment, by acting as decomposers and oxygen generators.</p>
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<p>Furthermore, they are very exploited in the biotechnology field, such as in food and beverage preparation, in water treatment, in energy production, in manufacturing of chemicals, enzymes and other bioactive molecules and in science. A small percentage of microorganisms are pathogenic and cause disease or even death in plants and animals, having, consequently, an important role in health.</p>
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<p>Sources:</p>
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<li><a href="http://www.sciencedaily.com/articles/m/microorganism.htm">http://www.sciencedaily.com/articles/m/microorganism.htm</a></li>
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<li>Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (13th ed.). Pearson Education. p. 1096. ISBN 0-321-73551-X.</li>
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<h3>Our Project</h3>
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<h3>Autotransporters</h3>
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<p>The mOrgan or micro-Organizer is a layered system for organizing E. coli in a predetermined and organ-like way.</p>
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<p>Wild type E.coli can express proteins on their surface by using a protein channeling system called an autotransporter. This proteins assemble themselves to a channel in the bacterial membrane and any proteins connected to them will be threaded through this channel and presented to the outside of the bacteria. The channel itself functions as a membrane anchor. We aimed to connect our split enzyme parts to the autotransporter and present them on the bacterial surface.</p>
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<p>This system can be applied in several fields of science and needs. In this context, the mOrgan is built up with different types of bacteria that form an organized structure and communicate to each other to perform specific functions, like organs.</p>
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<p>Thus, whatever is done in mOrgan occurs in a multi-step process within the different layers of the system.</p>
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<p>The E.coli will have a surface identity given by regulation of downstream genes and the mOrgan will be formed in an organized way. This property helps to avoid random bacteria linking to each other and creating uncontrolled growing colonies, keeping the correct configuration.</p>
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<h3>Applications</h3>
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<h3>Selection Mechanism</h3>
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<p>For instance, mOrgan can be useful in industrial manufacturing, industrial degradation, remediation processes, drug delivery systems, drug metabolism studies, catalytically amplified sensors, regulatory networks, biocomputers and so forth.</p>
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<p>By using a split enzyme which is active only when the different parts are assembled, the enzyme activity is an obvious marker of a succesful surface interaction between the bacteria. To succesfully establish a selection mechanism we also needed the bacteria to respond to the enzyme activity. We therefor wanted an enzyme which substrate could induce a particular response in the bacteria that the enzyme product could not. If the presence of the substrate could kill the bacteria and the presence of the product could not, the enzyme activity could protect the interacting bacteria and do the job as a selction mechanism.</p>
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<h3>The Details</h3>
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<p>We choose to use beta-galactosidase as our enzyme and beta-galactosyl glycerol as our substrate. Beta-galactosyl glycerol is a small beta-galatoside that can cross the E.coli membranes and enter cytoplasma through a constitutivly expressed galactose-permease. Beta-galactosyl glycerol can also bind to the lac-operon repressor in the same manner as allolactose and inhibit its repressor activity – thus function as an inducer of the lac-operon. Beta-galactosyl glycerol also makes a potential substrate for beta-galactosidase which splits beta-galactosyl glycerol into glucose and galactose1).</p>
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<p>A toxic gene under the control of the Lac-promoter would therefore kill cells that are not able to cleave beta-galactosyl glycerol.</p>
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<p>Beta-galactosidase is expressed in wild type E.coli from the Lac-Z gene which is a part of the Lac-operon. Beta-galactosidase can be split into two different parts with an intact tertiary structure and is therefore a good alternativ for our split enzyme. The two parts are coded by what has been called Lac-Z alpha and Lac-Z beta respectivly.</p>
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<p>The final version of the microorganizer system would be as follow. To different strains of bacteria would express a fusion protein consisting of the membrane part of an autotransporter and one of either Lac-Z alpha or Lac-Z beta. Both strains would also have a toxic gene under the control of the Lac-promoter. The two strains would be mixed in a medium containing beta-galactosyl glycerol. Bacteria with no partners would have beta-galactosyl glycerol flowing into cytoplasma and induce transcription from the Lac-promoter and kill them. Bacteria that are bound to each other through the beta-galactosidase parts will cleave galactosyl-glycerol into galactose and glucose and make sure the bacteria can survive.</p>
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<p>To avoid a short cut in the mechanism we would have to use bacteria were the Lac-operon is deleted so there is no cytoplasmic beta-galactosyl activity.</p>
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<h4>Sources</h4>
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<p>1) Egel, R. (1988) The "lac" operon: an irrelevant paradox? Trends in Genetics 4:31.</p>
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Revision as of 13:28, 17 October 2014

UiOslo IGEM 2014

Project Overview

Our Project - The microOrganizer

The aim of our project was to build a system for physically connecting different bacteria in a predetermined manner. Throughout the iGEM competition we have designed surface markers that enable bacteria to bind to each other and to respond to the binding by a mechanism that would allow us to select for bound bacteria. A succesful system would allow us to organize different types of bacteria in a culture and we have therefor named our project «The microOrganizer».

The Parts

Split Enzyme Principle

A split enzyme is an enzyme split into two or more non-functional parts with intact tertiary structure. This means that the enzyme can be active if the different parts come together and assemble into the original enzyme. The enzyme parts have a natural affinity for each other and can assemble spontanously. We wanted to expose two different parts of a split enzyme on the surface of different bacteria.

Autotransporters

Wild type E.coli can express proteins on their surface by using a protein channeling system called an autotransporter. This proteins assemble themselves to a channel in the bacterial membrane and any proteins connected to them will be threaded through this channel and presented to the outside of the bacteria. The channel itself functions as a membrane anchor. We aimed to connect our split enzyme parts to the autotransporter and present them on the bacterial surface.

Selection Mechanism

By using a split enzyme which is active only when the different parts are assembled, the enzyme activity is an obvious marker of a succesful surface interaction between the bacteria. To succesfully establish a selection mechanism we also needed the bacteria to respond to the enzyme activity. We therefor wanted an enzyme which substrate could induce a particular response in the bacteria that the enzyme product could not. If the presence of the substrate could kill the bacteria and the presence of the product could not, the enzyme activity could protect the interacting bacteria and do the job as a selction mechanism.

The Details

We choose to use beta-galactosidase as our enzyme and beta-galactosyl glycerol as our substrate. Beta-galactosyl glycerol is a small beta-galatoside that can cross the E.coli membranes and enter cytoplasma through a constitutivly expressed galactose-permease. Beta-galactosyl glycerol can also bind to the lac-operon repressor in the same manner as allolactose and inhibit its repressor activity – thus function as an inducer of the lac-operon. Beta-galactosyl glycerol also makes a potential substrate for beta-galactosidase which splits beta-galactosyl glycerol into glucose and galactose1).

A toxic gene under the control of the Lac-promoter would therefore kill cells that are not able to cleave beta-galactosyl glycerol.

Beta-galactosidase is expressed in wild type E.coli from the Lac-Z gene which is a part of the Lac-operon. Beta-galactosidase can be split into two different parts with an intact tertiary structure and is therefore a good alternativ for our split enzyme. The two parts are coded by what has been called Lac-Z alpha and Lac-Z beta respectivly.

The final version of the microorganizer system would be as follow. To different strains of bacteria would express a fusion protein consisting of the membrane part of an autotransporter and one of either Lac-Z alpha or Lac-Z beta. Both strains would also have a toxic gene under the control of the Lac-promoter. The two strains would be mixed in a medium containing beta-galactosyl glycerol. Bacteria with no partners would have beta-galactosyl glycerol flowing into cytoplasma and induce transcription from the Lac-promoter and kill them. Bacteria that are bound to each other through the beta-galactosidase parts will cleave galactosyl-glycerol into galactose and glucose and make sure the bacteria can survive.

To avoid a short cut in the mechanism we would have to use bacteria were the Lac-operon is deleted so there is no cytoplasmic beta-galactosyl activity.

Sources

1) Egel, R. (1988) The "lac" operon: an irrelevant paradox? Trends in Genetics 4:31.

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