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Revision as of 19:06, 26 September 2012

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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?

Fig. 1: Taken from [http://www.ncbi.nlm.nih.gov/pubmed/19554258 Kim, J. & Schumann W (2009)]. A: Cell at stage 0; vegetative phase. B: Cell at stage II; asymmetric septum has been formed. C: Cell at stage III; cytoplasmic membrane has engulfed forespore. D: Cell at stage IV; coat formation has started; spore will be released from lysed mother cell.

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.

Fig. 2: The germination process in Bacillus spores. Taken from [http://www.ncbi.nlm.nih.gov/pubmed/14662349 Setlow 2003].

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.

Fig. 3: Procedure of long-flanking homology PCR. As an example, replacement of cwlD by a kanamycin (kan) resistance cassette is shown. 1000 base-pair fragments flanking cwlD as well as the kan cassette were amplified. The up-reverse and down-forward primers have overhangs complementary to the kan cassette. The up and down clwD fragments and the amplified kan cassette were fused in a PCR reaction. The result is a fragment containing the kan cassette flanked by the up- and downstream region cwlD. B. subtilis is transformed with the fragment and the replacement of cwlD by the kan cassette is checked by PCR.

Fig. 4: Schematic representation of the B. subtilis chromosome with four germination genes replaced by different resistance cassettes. For more information about these knockout strains, please see our Strain Collection.

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 in our triple mutant B43. Other mutants also showed extremely reduced germination ability. A table of germination rates of our mutants and all other results can be found on our results page. Our single mutants were not checked in the germination assay. The double and triple mutants tested showed mixed results, with some unable to germinate, and others maintaining germination ability. Our quadruple mutants demonstrated no ability to germinate, even several separate germination assays.

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.

Suicideswitch

Fig. 5: Genetic elements of the Suicide switch and its expected performance.

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 and heterologous σ factor and the target promoter. Both are not present in B. subtilis and therefore not recognized by any other σ factor of B. subtilis.

The alternative sigma factor [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823043 ecf41_{Bli aa1-204}] ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426412/ Wecke T. et al 2012]), which derives from B. licheniformis a truncated version constitutively "ON" is synthetically linked to one out of two σ^G-regulated promoters ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K823048 P_spoIVB] ([http://www.ncbi.nlm.nih.gov/pubmed/15699190 Steil L. et al. 2005]) responding strongly or [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823042 P_sspK] ([http://www.ncbi.nlm.nih.gov/pubmed/15699190 Steil L., Völker U. et al. 2005]) responding weakly). σ^G is the last σ factor activated in the forespore. Consequently, Ecf41_{Bli aa1-204} is produced quite late and only in the forespore. Ecf41_{Bli aa1-204} then activates its unique target promoter [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823041 P_ydfG] ([http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426412/ Wecke T., Mascher T. 2012]). 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 P_ydfG therefore leads to the expression of MazF, a bacterial toxin from E.coli degrading mRNA.

The resulting time course of expression is as follows: Sporulation of the Sporobeads leads to Ecf41_{Bli aa1-204} production in the forespore at the end of the differentiation cycle, through the activation of either P_spoIVB or P_sspK. Subsequently, this would lead to the expression of MazF, due to the activation of P_ydfG. For our already matured Sporobeads, this would not be toxic, as they represent a dormant state that does not require translation any more. But in the case that a Sporobead escapes the Germinationstop based on the gene knockouts described above, a germinating cell will already contain or soon start producing MazF and therefore kill the vegetative cells.

See what Data we got when measuring a module with luxABCDE instead of MazF.

We are planning to model this system, but still need more quantitative, time-resolved data for it. We hope to get this data after finishing the cloning of P_sspK and MazF into B. subtilis.