From 2012.igem.org

Revision as of 00:36, 24 September 2012

• Home
• Team
  • Members
  • Official Profile
  • The University
  • Outtakes
  • Contact Us
• Project
  • Overview
    • Data Page
    • Accomplishments
    • Post-Regionals
  • Human Practices
    • Initiative
    • Interviews
    • Design
    • Killswitch
    • Regulation
    • Kill Genes
    • Safety
  • FRED
    • Toxin Sensing
    • Electroreporting
    • Modelling
    • Device Prototype
  • OSCAR
    • Decarboxylation
    • Decatecholization
    • Flux Analysis
    • Bioreactor
    • Upgrading
    • Desulfurization
    • Denitrogenation
  • Synergy
  • References
  • Attributions
• Parts
• Notebook
  • Journal
  • Protocols
• Outreach
  • LAB ESCAPE!
  • Spark Science
  • Minds in Motion
  • Blog Posts
  • TEDxCalgary
  • Follow Us!
• Sponsors
• iGEM

Purpose:

Synthetic biology entails designing an organism to do a specific task. This involves genetic manipulation and requires scientists to provide the bacteria with a selective advantage such as an antibiotic cassette which forces the bacteria to keep the gene of interest inside the cell. With such manipulation comes a valid “risk of accidental release” (Tucker and Zilinkas, 2006). In order to prevent such a bacteria from becoming rogue a killswitch is designed such that the bacteria is only able to survive in specific environments allowing them to perform the tasks of decarboxylation, denitrification and desulfurization in our bioreactor. However, in case of these bacteria escaping, the lack of a metabolite and or the presence of a particular metabolite will activate the “kill genes” which will cause the bacteria to self destruct. The killswitch mechanism was put in our system as a safety measure in addition to the bioreactor to contain the synthetic bacteria.

History:

Scientists have been trying to develop methods to limit bacterial viability and growth outside of the lab environment. One of the most popular methods used to ensure the safety of bacteria used in the lab was the creation of lab strain bacteria such as DH5α and Top10. These bacteria are metabolically deficient and are unable to survive outside of the lab environment without very specific nutrients. Additionally, The Registry of Biological Parts also has several killswitches readily available that were submitted by previous iGEM teams.

The different types of killswitches include:

Inducible kill genes:

Inducible systems generally consist of a regulatory element such as a promoter which is activated in the presence or absence of a metabolite. GIVE EXAMPLES

Toxin-antitoxin systems:

These systems usually insert antitoxin in the plasmid and toxin in the genome. Ideally if the bacteria lose the plasmid then the bacteria dies. This does not address the problem of horizontal gene transfer between species.

Auxotrophic marker

Design considerations:

During the first phase of design we considered classic systems such as auxotrophic markers, toxin-antitoxin systems, inducible systems. However, considering the cost of the system if auxotrophic markers were used we did not pursue that route. We have decided to use the inducible systems. We explored four different inducible systems which are induced by inexpensive ligands such as magnesium, manganese, molybate salts and glucose. In order to make sure the systems are controlled well and the kill switch regulation is not leaky, we have added an additional control using the riboswitch.

A riboswitch provides post-transcriptional control of gene expression. A riboswitch is a small stretch of mRNA which binds to a ligand which increases or decreases the expression of the gene downstream.

INSERT IMAGE OF RIBOSWITCH

Our kill genes:

The kill genes used in this project are S7 endonuclease from Staphylococcus aureus and a type II restriction enzyme from chlorella virus PCBV-1 called CviAII.

S7 endonuclease

S7 endonuclease is the protein product of the gene nucA from staphylococcus aureus. This endonuclease was selected due to its ability to function in low temperatures. Due to the weather in Alberta, we chose an enzyme which is able to function at low temperatures. S7 nuclease is known to function at temperature of zero degrees. FIND CITATION. Micrococcal nuclease is cleaves A-T rich regions rather than G-C rich regions (Dingwall et al, 1981). Another advantage of using this gene is the associated kinetics. This enzyme is shown to degrade genomes in less than an hour (FIND REFERENCE).

CviAII

is a restriction enzyme which cleaves DNA at the sequence CATG. TALK ABOUT KINETICS, TALK ABOUT WHY THIS WILL PROVIDE AN ADVANTAGE

Nuclease assay to evaluate the nucleases present in the registry (BglII and BamHI):

Regulation of our kill genes:

Glucose repression:

This system entails the use of a promoter called rhamnose promoter (pRha). The rhamnose promoter is repressed in presence of glucose (≥0.2%), has leaky expression in the absence of glucose and is highly upregulated in the presence of a sugar called rhamnose. In this system, the presence of rhamnose activates expression of rhaR which increases in turn expresses rhaS and rhaR. Finally, rhaS binds to pRHA in the presence of rhamnose and causes expression of the rhaBAD operon. PUT GRAPH. This system will be suppressed in the bioreactor which will contain bacterial growth medium containing glucose. This will suppress the expression of kill genes and allow our cells to perform their respective functions such as decarboxylation, denitrification and desulfurization. Ideally, if the bacteria do escape from the bioreactor into the tailings pond the lack of glucose would activate the expression of the kill genes which would destroy the bacterial genome stopping it from not only propagating in the environment but also passing on genes to other bacteria in the environment.

Magnesium regulation

This system is repressed in the presence of magnesium. This system has two control components – a promoter and a riboswitch. Normally the magnesium promoter (mgtA promoter) and the magnesium riboswitch (mgtArb) are activated if there is a deficiency of magnesium in the cell. The lack of magnesium normally activates other genes in E. coli to bring in more magnesium into the cell. There are two proteins in the cascade that activate the system namely PhoP and PhoQ. PhoQ is the trans-membrane protein which gets activated in the absence of magnesium and phosphorylates PhoP. PhoP in turn binds to the mgtA promoter and transcribes genes downstream.

Manganese regulation

The manganese system engages a promoter and a riboswitch. However this system operates in a reciprocal manner compared to the magnesium system. This system allows expression of the system downstream

Molybdate co-factor protein regulation