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Team:LMU-Munich/Germination Stop
From 2012.igem.org
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==How do Germination Gene Knockouts Work?== | ==How do Germination Gene Knockouts Work?== | ||
| - | <p align="justify">Based on the | + | <p align="justify">Our idea of how to prevent germination from occurring is to knock out genes involved in the germination process. There are a huge number of genes which play a role in germination, but our goal was to select a few very essential genes to knock out.</p> |
| + | <p align="justify">Based on the research of others, the genes we chose were ''cwlJ'', ''sleB'', ''cwlB'', ''gerD'', and ''cwlD''. Past works of [http://www.ncbi.nlm.nih.gov/pubmed/19554258 J. Kim and W. Schumann (2009)] and [http://www.ncbi.nlm.nih.gov/pubmed/11466293 B. Setlow et al (2001)] showed:</p> | ||
*'''''cwlJ'' and ''sleB''''': both genes code for lytic enzymes which are active in the process of germination. When knocked out together, germination frequency was reduced by 5 orders of magnitude. | *'''''cwlJ'' and ''sleB''''': both genes code for lytic enzymes which are active in the process of germination. When knocked out together, germination frequency was reduced by 5 orders of magnitude. | ||
*'''''gerD'' and ''cwlB''''': the ''gerD'' product plays an unknown role in nutrient germination; the product of ''cwlB'' plays a role in cell wall turnover & cell lysis. When knocked out together, germination frequency was reduced by 5 orders of magnitude. Note: after several attempts to knock out ''cwlB'', and yielding cells unable to grow or cells growing at a very slow rate, we determined that knocking out ''cwlB'' would not be prudent for the production of [https://2012.igem.org/Team:LMU-Munich/Spore_Coat_Proteins '''Sporo'''beads], as it would delay all experiments in the '''Germination'''STOP module. | *'''''gerD'' and ''cwlB''''': the ''gerD'' product plays an unknown role in nutrient germination; the product of ''cwlB'' plays a role in cell wall turnover & cell lysis. When knocked out together, germination frequency was reduced by 5 orders of magnitude. Note: after several attempts to knock out ''cwlB'', and yielding cells unable to grow or cells growing at a very slow rate, we determined that knocking out ''cwlB'' would not be prudent for the production of [https://2012.igem.org/Team:LMU-Munich/Spore_Coat_Proteins '''Sporo'''beads], as it would delay all experiments in the '''Germination'''STOP module. | ||
Revision as of 17:34, 26 September 2012
The LMU-Munich team is exuberantly happy about the great success at the World Championship Jamboree in Boston. Our project Beadzillus finished 4th and won the prize for the "Best Wiki" (with Slovenia) and "Best New Application Project".
[ more news ]
GerminationSTOP
The goal of this module was to yield Sporobeads which are safe (unable to germinate) and consistently functional (maintain their spore shape and structure throughout time). To achieve this, we sought to remove the germination capability of our spores, while keeping their necessary structural functions intact.
Two approaches were used to achieve this:
- Knock out genes that are involved in germination.
- Suicide switch: Toxin production by vegetative cells if germination knockout fails and spores manage to germinate.
How do Sporulation & Germination Work?
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The Bacillus life cycle can include both classic division as well as reproduction by sporulation and spore germination. In response to starvation of nutrients (including carbon, nitrogen, or phosphorus) or in response to peptides secreted by other cells which signal high population densities, Bacillus cells form spores in a process called sporulation (Fig. 1). The “mother” cell forms the endospore within its own cell membrane. The endospore contains its DNA in the spore core, which is protected by several layers of coats. The outermost layer is the spore crust. The spore is very dry, and contains a substance called dipicolinic acid (DPA), which is replaced with water when the spore germinates. Until the spore hydrates and swells out of its protective coats, it is resistant to a wide variety of environmental stressors, including UV radiation, toxic chemicals, freezing, high heat, dessication, and pH extremes. This resistance to stressors allows the spore to survive until conditions are good for growth.
On its inner spore membrane, the spore has germinant receptors. The spore coats are believed to be semipermeable or porous, in order to permit the passage of germinants to the receptors. When germinants such as amino acids and sugars reach the receptors, the spore begins the biochemical process of germination (see Fig. 2). During germination, the spore replaces its DPA with water (Stages I and II in Fig. 2), shifts its pH (Stage I), and swells (Stage II). Lytic enzymes break down the rigid spore coat layers encapsulating the spore's core (Stage II), allowing the spore core to swell further and begin the outgrowth process into a vegetative cell(Outhgrowth). When the spore coat is broken down by lytic enzymes, the spore's environmental resistance is lost. For our project, we wish to prevent the germination process.
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How do Germination Gene Knockouts Work?
Our idea of how to prevent germination from occurring is to knock out genes involved in the germination process. There are a huge number of genes which play a role in germination, but our goal was to select a few very essential genes to knock out.
Based on the research of others, the genes we chose were cwlJ, sleB, cwlB, gerD, and cwlD. Past works of [http://www.ncbi.nlm.nih.gov/pubmed/19554258 J. Kim and W. Schumann (2009)] and [http://www.ncbi.nlm.nih.gov/pubmed/11466293 B. Setlow et al (2001)] showed:
- cwlJ and sleB: both genes code for lytic enzymes which are active in the process of germination. When knocked out together, germination frequency was reduced by 5 orders of magnitude.
- gerD and cwlB: the gerD product plays an unknown role in nutrient germination; the product of cwlB plays a role in cell wall turnover & cell lysis. When knocked out together, germination frequency was reduced by 5 orders of magnitude. Note: after several attempts to knock out cwlB, and yielding cells unable to grow or cells growing at a very slow rate, we determined that knocking out cwlB would not be prudent for the production of Sporobeads, as it would delay all experiments in the GerminationSTOP module.
- cwlD: this gene codes for recognition components for cleavage by the germination-specific cortex lytic enzymes. When knocked out, germination occurred at a rate of 0.003 to 0.05%.
By knocking out all five of these genes, our goal was to yield a B. subtilis strain which produces spores completely incapable of germination. Germination is stopped during the process of spore coat breakdown. Without the lytic enzymes to break down the coat, the spores should be unable to outgrow into the vegetative stage. After several attempts to knock out cwlB, and producing extremely slow-growing mutants, cwlB was removed from our list of genes to knock out.
| Germination Genes | Gene Function | Mutant Germination Rate |
|---|---|---|
| gerD | Unknown role in nutrition germination | Reduction by 5 orders of magnitude |
| cwlJ | Germination-specific lytic enzymes | 0.003 – 0.05%
No ATP detected |
| sleB | Germination-specific lytic enzymes | 0.003 – 0.05%
No ATP detected |
| cwlD | Recognition component for lytic enzymes | 0.003 – 0-005% |
What Methods Did We Use to Knockout Germination Genes?
Two methods were employed to knock out germination genes: replacement by resistance cassettes and clean deletions. Resistance cassette (RC) knockouts were performed using long-flanking homology PCR (see Fig. 3 and Protocols). Single RC knockouts were created first; then they were combined to create multiple knockouts. A graphical representation of the genome with all replacements with resistance cassettes can be seen in Fig 4.
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The germination rate of our mutants were checked with a germination assay. The assay was developed based on the protocols of other researchers.
We were able to achieve germination rates as low as <1 in 4.6x109 spores for some mutants. A table of germination rates of different mutants and all other results can be found on our results page.
Despite this success, safety was a top priority for this project. In the event that some small percentage of spores retained the ability to germinate, the Suicide switch subproject (below) prevents outgrowth into viable vegetative cells.
Suicide switch
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As a backup plan to make our Sporobeads even safer, we developed the Suicideswitch. In case the spores do germinate, due to degradation or destruction of their outer coats, e.g. by high pressure, the Suicideswitch will be turned on.
We take advantage of an alternative σ factor and a promoter regulated by it both not present in B. subtilis and therefore not recognised by any other σ factor of B. subtilis.
The alternative sigma factor [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823043 ecf41Bli aa1-204] ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426412/ Wecke T., Mascher T. 2012]), which derives from B. lincheniformes a truncated version constitutively on is synthetically linked to a sigma G regulated promotor responding quite late to σG ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K823048 PspoIVB] ([http://www.ncbi.nlm.nih.gov/pubmed/15699190 Steil L., Völker U. et al. 2005]) responding strongly or [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823042 PsspK] ([http://www.ncbi.nlm.nih.gov/pubmed/15699190 Steil L., Völker U. et al. 2005]) responding weakly). σG is the last σ factor activated in the forespore. Consequently ecf41Bli aa1-204 is produced quite late in the forespore. ecf41Bli aa1-204 then activates the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823041 PydfG] ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426412/ Wecke T., Mascher T. 2012]) promotor, which is the only target promoter of ecf41Bli aa1-204. This promoter is fused to [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823044 MazF] ([http://jcs.biologists.org/content/118/19/4327.abstract Engelberg-Kulka H.,Amitai S. 2005]). Activation of PydfG therefore leads to the expression of MazF, a bacterial toxin from E.coli degrading mRNA.
The timecourse is as follows: Sporulation of the Sporobeads leads to ecf41Bli aa1-204, through the activation of either PspoIVB or PsspK. This then would lead to the expression of MazF over the activation of PydfG. This is either not toxic to the Sporobeads, as they do not rely on translation, or not produced any more by the Sporobeads as they are mature spores. After Germination MazF will then be produced for sure and kill the vegetative cell
See what Data we get when measuring a module with luxABCDE instead of MazF.
We are planning to model this system, but still need some data for it. We will get this data after finishing the cloning of PsspK and MazF into B. subtilis.
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| Bacillus Intro | Bacillus BioBrickBox | Sporobeads | Germination STOP |
