Team:Goettingen/Achievement

From 2013.igem.org

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Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
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collaborated with Team Groningen in Netherland, and provided two soil samples for Team Norvich.
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==We apply for==
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Best BioBrick Measurement Approach
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Best Model
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The progress in the development of new antibiotics has been very slow during the last decades, leaving many strains of bacteria untreatable. This problem has been growing ever since the invention of antibiotics but has now become a real threat to millions of people around the world. This Threat we want to tackle with a new approach: We develop a system to test substances on a new target, cyclic-di-AMP.
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C-di-AMP was discovered to be an essential signaling molecule in Gram-positive bacteria including the pathogens Streptococcus pneumoniae, Staphylococcus aureus and Listeria monocytogenes. Both loss and overproduction of c-di-AMP have detrimental effects on cell growth, cell wall synthesis and propagation.
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'''Best Biobrick Measurement Approach: '''
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Thus, the diadenylate cyclase (DAC) which catalyses the condensation reaction of 2 ATP molecules to c-di-AMP is the key factor for c-di-AMP homeostasis. We are convinced that the DAC protein is a very promising target for the development of highly specific antibiotic substances which exclusively act on Gram-positive bacteria and are not harming Gram-negative ones, including the gut bacterium Escherichia coli as well as humans. We characterized the DAC in vivo and in vitro. Here, we introduce a truncated but functional DAC, which localizes to the cytosol and can easily be purified. Furthermore, we obtained protein crystals and the protein structure by X-ray diffraction analysis. For the first time ever the 3D structure for this cyclase, which is conserved among all important Gram-positive bacteria, was resolved. This structure will be an important starting point for bioinformatic docking studies (BBa_K1045003)
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'''Best Model Approach: '''
 +
 
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To test an antibiotic on the new target, we isolated (as mentioned above) the truncated DAC and did activity measurements on it. Using this data, we can now screen thousands of substances for impacts on the function of the DAC (''in silico'' and ''in vitro'' screening). Furthermore, we created in vivo reporter systems in E. coli, giving us the ability to sense the amount of c-di-AMP inside the cells, as well as to find possible inhibitors or competitors for c-di-AMP. Last but not least, the combination of the two: An ''in vivo'' reporter system with the DAC expressed in the same cell will be the c-di-AMP pathway from Gram-positive bacteria, reconstructed in E. coli. This way, it will be ready to screen for substances lethal to it´s Gram-positive relatives, without harming our host. In consequence, our model will facilitate the search for novel antibiotics hitting a novel target in Gram-positive bacteria.
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==About our parts==
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We have two new parts built, namely:  [http://partsregistry/Part:BBa_K1045003 BBa_K1045003],[http://partsregistry/Part:BBa_K1045017  BBa_K1045017]
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We also improved some parts, one of them is  [http://partsregistry/Part:BBa_K1045011 BBa_K1045011]
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 +
We did qRT PCR analysis, single cell microscopy and RFP analyses in different growth phases of the original part BBa_J23117. These measurements contribute to a highly increased characterization of this part and three others from it´s promoter family. We also inverted this part, thus improving it and making it usable in an inverted expression unit. This we used in order to express our repressor DarR on the same vector as our reporter system. The improved part submitted to the registry is BBa_K1045011.
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<html>
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</div>

Revision as of 16:54, 3 October 2013





The beast and its Achilles heel:

 A novel target to fight multi-resistant pathogenic bacteria


Contents

Team: Goettingen

Region: Europe

iGEM Year: 2013

Track: Health & Medicine

Project Name: The beast and its Achilles heel: A novel target to fight multi-resistant bacteria


Project Abstract:

Since the discovery of penicillin by Alexander Fleming in 1928, antibiotics have marked a major victory of mankind in the battle against infectious diseases. However, after 90 years, the antibiotics are now losing their old time glory: Bacteria acquire resistance against antibiotics and become unbridled. We must control the use of antibiotics, meanwhile, we need new antibiotics, which can sufficiently eliminate the invaders without hurting the "good" bacteria. Therefore, c-di-AMP, an important, recently discovered signaling molecule in gram-positive bacteria, has come to our sight. Our project is to build a screening system targeting c-di-AMP, which could be applied in novel-drug screening. With this system, the level of c-di-AMP in the cell can be visualized and measured.


Achievements

We have:

Goe-%E2%88%9A.JPEG Register the team, have a great summer, and plan to have fun at the Regional Jamboree.

Goe-%E2%88%9A.JPEG Successfully complete and submit this iGEM 2013 Judging form.

Goe-%E2%88%9A.JPEG Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts.

Goe-%E2%88%9A.JPEG Plan to present a Poster and Talk at the iGEM Jamboree.

Goe-%E2%88%9A.JPEG Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). A new application of, and outstanding documentation (quantitative data showing the Part's/ Device's function), of a previously existing BioBrick part in the 'Experience' page of that part's Registry entry also counts. Please note you must submit this new part to the iGEM Registry.

For all our parts, we have accomlished:

Goe-%E2%88%9A.JPEG Description of function

Goe-%E2%88%9A.JPEG Quantitative data showing the Part or Device function

Goe-%E2%88%9A.JPEG Acknowedgment of sources and references



We have also:

Goe-%E2%88%9A.JPEG experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.

Goe-%E2%88%9A.JPEG document the characterization of this part in the 'Main Page' of that Part's/Device's Registry entry. Submit new parts to the iGEM Parts Registry.

For our parts, we have also fulfilled

Goe-%E2%88%9A.JPEG Description of function

Goe-%E2%88%9A.JPEG Quantitative data showing the Part or Device function

Goe-%E2%88%9A.JPEG Acknowedgment of sources and references

Goe-%E2%88%9A.JPEG considered the safety issues and filled in the safe forms.




We have also:

Goe-%E2%88%9A.JPEG improve the function of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the 'Experience' section of that Parts's Registry entry), create a new registry page for the improved part, and submit this part to the iGEM Registry. See Parts

For all improved parts, we fulfilled:

Goe-%E2%88%9A.JPEG Description of function

Goe-%E2%88%9A.JPEG Quantitative data showing the Part or Device function

Goe-%E2%88%9A.JPEG Acknowedgment of sources and references

Goe-%E2%88%9A.JPEG collaborated with Team Groningen in Netherland, and provided two soil samples for Team Norvich.

We apply for

Best BioBrick Measurement Approach

Best Model


The progress in the development of new antibiotics has been very slow during the last decades, leaving many strains of bacteria untreatable. This problem has been growing ever since the invention of antibiotics but has now become a real threat to millions of people around the world. This Threat we want to tackle with a new approach: We develop a system to test substances on a new target, cyclic-di-AMP.

C-di-AMP was discovered to be an essential signaling molecule in Gram-positive bacteria including the pathogens Streptococcus pneumoniae, Staphylococcus aureus and Listeria monocytogenes. Both loss and overproduction of c-di-AMP have detrimental effects on cell growth, cell wall synthesis and propagation.

Best Biobrick Measurement Approach:

Thus, the diadenylate cyclase (DAC) which catalyses the condensation reaction of 2 ATP molecules to c-di-AMP is the key factor for c-di-AMP homeostasis. We are convinced that the DAC protein is a very promising target for the development of highly specific antibiotic substances which exclusively act on Gram-positive bacteria and are not harming Gram-negative ones, including the gut bacterium Escherichia coli as well as humans. We characterized the DAC in vivo and in vitro. Here, we introduce a truncated but functional DAC, which localizes to the cytosol and can easily be purified. Furthermore, we obtained protein crystals and the protein structure by X-ray diffraction analysis. For the first time ever the 3D structure for this cyclase, which is conserved among all important Gram-positive bacteria, was resolved. This structure will be an important starting point for bioinformatic docking studies (BBa_K1045003)

Best Model Approach:

To test an antibiotic on the new target, we isolated (as mentioned above) the truncated DAC and did activity measurements on it. Using this data, we can now screen thousands of substances for impacts on the function of the DAC (in silico and in vitro screening). Furthermore, we created in vivo reporter systems in E. coli, giving us the ability to sense the amount of c-di-AMP inside the cells, as well as to find possible inhibitors or competitors for c-di-AMP. Last but not least, the combination of the two: An in vivo reporter system with the DAC expressed in the same cell will be the c-di-AMP pathway from Gram-positive bacteria, reconstructed in E. coli. This way, it will be ready to screen for substances lethal to it´s Gram-positive relatives, without harming our host. In consequence, our model will facilitate the search for novel antibiotics hitting a novel target in Gram-positive bacteria.



About our parts

We have two new parts built, namely: [http://partsregistry/Part:BBa_K1045003 BBa_K1045003],[http://partsregistry/Part:BBa_K1045017 BBa_K1045017]

We also improved some parts, one of them is [http://partsregistry/Part:BBa_K1045011 BBa_K1045011]

We did qRT PCR analysis, single cell microscopy and RFP analyses in different growth phases of the original part BBa_J23117. These measurements contribute to a highly increased characterization of this part and three others from it´s promoter family. We also inverted this part, thus improving it and making it usable in an inverted expression unit. This we used in order to express our repressor DarR on the same vector as our reporter system. The improved part submitted to the registry is BBa_K1045011.

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