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GerminationSTOP

The goal of this subproject 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 a 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. It takes up water, shifts its pH, and swells. It breaks out of its coat and begins the outgrowth process (see Fig. 2). 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?

Based on the work of others, we chose to knock out genes cwlJ, sleB, cwlB, gerD, and cwlD. Past works 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 unknown role in nutrient germination; cwlB's product plays 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. The stop to germination comes 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 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

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 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 ecf41_{Bli 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 σ^G ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K823048 P_spoIVB] ([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 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 in the forespore. ecf41_{Bli aa1-204} then activates the [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]) promotor, which is the only target promoter of ecf41_{Bli 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 P_ydfG 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 ecf41_{Bli aa1-204}, through the activation of either P_spoIVB or P_sspK. This then would lead to the expression of MazF over the activation of P_ydfG. 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 P_sspK and MazF into B. subtilis.