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Meetings Calendar

Sporulation Tuning

Introduction

The bacterium Bacillus subtilis used in our project is a gram-positive soil bacterium which, under certain conditions, commits itself to a developmental pathway leading to the production of spores.^[1] In this part of our project, we aim to control sporulation in our bacterial population, so that we can decide how much of the population becomes spores, and how much continue as vegetative cells. Should the cell sporulate, it becomes a ‘metal container’, trapping the sequestered cadmium in its spore.

After the cell sequesters cadmium into its spore, it should not germinate, or the sequestered cadmium will be released back into the environment. Therefore, the chassis comes into play, where the sleB and cwlJ germination-defective mutants are put into use.

In order to control sporulation, our team proposed the idea of inducing the synthesis of kinA, with IPTG as a sporulation initiation signal.

KinA is a major kinase which provides phosphate input to a phosphorelay, which in turn, activates the sporulation pathway upon starvation via the phosphorylated Spo0A transcription factor,^[2] which governs entry into the sporulation pathways of the bacterium Bacillus subtilis.^[3]

... Click to read more ...

Novelty in this sub-project

In this sub-project, instead of allowing the cell to decide whether or not to sporulate, we influence its decision. In order to execute our plan, we used the concentration of kinA, induced by IPTG, to control sporulation.

This sub-project consists of two main models: the Sporulation Tuning and the Sin Operon models. These two models are meant to work together, as mentioned below in the modelling section, with the Sporulation Tuning model controlling sporulation, and the Sin Operon model repressing sporulation, creating a more realistic model.

Modelling

The Sin (sporulation inhibition) Operon Model was one of the earlier models built. As its name suggests, it models the repression of sporulation. The Sin Operon Model was built in CellML.

The second model built was the simple model of KinA expression. After satisfactory results were obtained, the sporulation phosphorelay was modelled into the KinA Expression Model, and is known as the Sporulation Tuning Model. Both the KinA Expression and Sporulation Tuning models were built using COPASI.

The Sin Operon and Sporulation Tuning model work hand in hand as components of the Population Dynamics model.

KinA Expression Model

Under normal conditions, LacI represses kinA.

However, in the presence of IPTG, KinA can be expressed, as IPTG binds to lacI, deactivating it. Equations (a) and (b) describes how IPTG binds to LacI, forming LacI*, which is the deactivated form of LacI

Click to view more of the KinA Expression Model equations

Results

Click to view the KinA Expression results

Sporulation Tuning Model

The expression of KinA has been modelled as seen above, therefore we can now proceed further into the Sporulation Tuning Model, which is built from the KinA Expression Model using COPASI.

To proceed with the modelling of our Sporulation Tuning Model, we have decided that in response to an unidentified stimulus, where KinA autophosphorylates and then donates its phosphate groups to the response regulator Spo0F, the unidentified stimuli will be termed as 'sporulation signal'.^[5]

The following equations describe the model:

Equation 1

Equation 2

Equation 3

Click to view more of the Sporulation Tuning Model equations

Results

Click to view the Sporulation Tuning results

Sin (sporulation inhibition) Operon Model

In order to create a more realistic model of our sporulation system the team has decided to include the Sin (sporulation inhibition) Operon Model, which the team designed in CellML.

The sin operon controls the production and activity of the repressor SinR, which in its active tetrameric form, inhibits sporulation by repressing stage II and spo0A promoters. On the other hand, the accumulation of Spo0A~P induces the expression of SinI, which binds to and inactivates SinR.

Diagram 1: Simplifed Schematic of the sin Operon^[9]

Click to view more of the Sin Operon Model equations

Results

Click to view the Sin Operon Model results

BioBrick constructs

The BioBrick we have designed is to contain an IPTG inducable kinA gene, using pSpac, allowing us to test the theory about KinA in the lab.

BBa_K174010

KinA

Length: 1818bp

Click here for more information on this part.

BBa_K174011

IPTG inducable KinA sporulation trigger

Length: 1953bp

Click here for more information on this part.

Lab Work Strategies

The lab work executed was be to induce sporulation in the presence of IPTG, and this involved microscopy and testing cultures for sporulation (e.g. by their heat resistance).

To find out more about our lab work strategies,

see Lab Work Strategies

References

[1] Predich, M., Nair, G., Smith, I. (1992) Bacillus subtilis Early Sporulation Genes kinA, spo0F, and spo0A Are Transcribed by the RNA Polymerase Containing σ^H. Journal of Bacteriology. Pp 2771-2778

[2] Veening, J-W., Smits, W. K., Kuipers, O. P. (2008) Bistability, Epigenetics, and Bet-Hedging in Bacteria. Annu. Rev. Microbiol. 62: 193-210

[3] Fujita, M., Losick, R. (2005) Evidence that Entry into Sporulation in Bacillus subtilis is Governed by a Gradual Increase in the Level and Activity of the Master Regulator Spo0A. 19: 2236–2244

[4] Sonenshein, A.L., Hoch, J.A., Losick, R., (2002) Bacillus subtilis and Its Closest Relatives From Genes to Cells. ASM Press, United States of America. Pp 476–477

[5] Hilbert, D.W., Piggot, P.J., (June 2004) Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation. Microbiology and Molecular Biology Reviews. Vol. 68, No. 2. Pp 234-262

[6] Eswaramoorthy, P., Guo, T., Fujita, M. (2009) In Vivo Domain-Based Functional Analysis of the Major Sporulation Sensor Kinase, KinA, in Bacillus subtilis. Journal of Bacteriology. Pp 5358-5368

[7] Stephenson, K., Hoch, J. A. (2001) PAS-A domain of phosphorelay sensor kinase A: A catalytic ATP-binding domain involved in the initiation of development in Bacillus subtilis. PNAS. Vol. 98, no. 26: 15251-15256

[8] Veening, J-W., Hamoen, L. W., Kuipers, O. P. (2005) Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis. Molecular Microbiology 56(6), 1481-1494

[9] Voigt, C. A., Wolf, D. M., Arkin, A. P. (2004) The Bacillus subtilis sin Operon: An Evolvable Network Motif. Genetics 169: 1187-1202

@@ Line 7: / Line 7: @@
 ==Introduction==
-In this section of our project, we hope to control sporulation in our bacterial population, such that we can decide how much of the population becomes spores, and how much continue as vegetative cells. Should the cell sporulate, it would become a ‘metal container’, trapping the sequestered cadmium in its spore.
+The bacterium ''Bacillus subtilis'' used in our project is a gram-positive soil bacterium which, under certain conditions, commits itself to a developmental pathway leading to the production of spores.<sup>[1]</sup> In this part of our project, we aim to control sporulation in our bacterial population, so that we can decide how much of the population becomes spores, and how much continue as vegetative cells. Should the cell sporulate, it becomes a [https://2009.igem.org/Team:Newcastle/Metalintakeefflux ‘metal container’], trapping the sequestered cadmium in its spore.
-After the cell sequesters cadmium into its spore, it should not germinate or the sequestered cadmium will be released back into the environment as a result. Therefore, the role of chassis comes into play, where the sleB and cwlJ germination-defective mutants are put into use. More information about this other sub-project of ours can be found [https://2009.igem.org/Team:Newcastle/Chassis ''here''].
+After the cell sequesters cadmium into its spore, it should not germinate, or the sequestered cadmium will be released back into the environment. Therefore, the [https://2009.igem.org/Team:Newcastle/Chassis chassis] comes into play, where the ''sleB'' and ''cwlJ'' germination-defective mutants are put into use.
-In order to control sporulation, our team is proposing the idea of inducing the synthesis of KinA, with IPTG as a sporulation initiation signal.
+In order to control sporulation, our team proposed the idea of inducing the synthesis of ''kinA'', with IPTG as a sporulation initiation signal.
-KinA is a major kinase which provides phosphate input to the phosphorelay, which in turn, activates the sporulation pathway upon starvation via the phosphorylated Spo0A transcription factor,<sup>[1]</sup> which governs entry into the sporulation pathways of the bacterium Bacillus subtilis.<sup>[2]</sup>
+[https://2009.igem.org/Team:Newcastle/SporulationTuning/Introduction#KinA ''KinA''] is a major kinase which provides phosphate input to a phosphorelay, which in turn, activates the sporulation pathway upon starvation via the phosphorylated Spo0A transcription factor,<sup>[2]</sup> which governs entry into the sporulation pathways of the bacterium ''Bacillus subtilis''.<sup>[3]</sup>
+:''[[Team:Newcastle/SporulationTuning/Introduction#Spo0A| ... Click to read more ...]]
-===Spo0A===
+<br>
-From our research, we found that entry into the sporulation pathway is governed by a member of the response regulator family of transcription facts, known as Spo0A.<sup>[2]</sup> Spo0A is activated by [https://2009.igem.org/Team:Newcastle/SporulationTuning/Phosphorylation phosphorylation] on an aspartyl residue located in the N-terminal portion of the protein.<sup>[2]</sup>
+==Novelty in this sub-project==
-Unlike other response regulators, Spo0A is indirectly phosphorylated by a multicomponent phosphorelay involving at least three kinases called KinA, KinB, and KinC, which phosphorylate Spo0F, and the resulting Spo0F~P, in turn, transfers the phosphoryl group to Spo0B. Finally, Spo0B~P transfers the phosphoryl group to, and thereby activates, Spo0A.<sup>[2]</sup> As such, the phophoryl groups are drained from the relay by the action of dedicated phosphotases that dephosphorylate Spo0F~P and Spo0A~P.<sup>[2]</sup>
+In this sub-project, instead of allowing the cell to decide whether or not to sporulate, we influence its decision. In order to execute our plan, we used the concentration of ''kinA'', induced by IPTG, to control sporulation.
-Spo0A is also subjected to control at the levels of its synthesis and activity by a positive feedback loop in which the response regulator stimulates the synthesis of the RNA polymerase σ factor σH, which, in turn stimulates transcription of the gene for Spo0A, as well as the genes for the phosphorelay components KinA and Spo0F.<sup>[1]</sup>
+This sub-project consists of two main models: the Sporulation Tuning and the Sin Operon models. These two models are meant to work together, as mentioned below in the [https://2009.igem.org/Team:Newcastle/SporulationTuning#Modelling modelling section], with the Sporulation Tuning model controlling sporulation, and the Sin Operon model repressing sporulation, creating a more realistic model.
-It is important to note that activating Spo0A via the phosphorelay is essential as it is responsible for allowing Spo0A to accumulate in a gradual manner, and this slow accumulation plays a critical role in the ability of the regulatory protein to trigger sporulation.<sup>[2]</sup> Experiments have also been carried out and results have shown that the activated form of Spo0A failed to trigger sporulation during growth as it had bypassed phosphorylation, and only a small proportion of cells progressed to the early stage of sporulation.<sup>[2]</sup>
+==Modelling==
+The Sin (sporulation inhibition) Operon Model was one of the earlier models built. As its name suggests, it models the repression of sporulation. The Sin Operon Model was built in CellML.
-===Sporulation===
+The second model built was the simple model of KinA expression. After satisfactory results were obtained, the sporulation phosphorelay was modelled into the KinA Expression Model, and is known as the Sporulation Tuning Model. Both the KinA Expression and Sporulation Tuning models were built using COPASI.
-From our research, we found that phosphatases may be viewed as negative regulators that provide access for negative signals to influence the cell’s decision whether to sporulate or to continue vegetative growth.<sup>[3]</sup> The phosphotases that dephosphorylates Spo0A, preventing its activation are Spo0E, YisI, and YnzD.<sup>[4]</sup>
+The Sin Operon and Sporulation Tuning model work hand in hand as components of the [https://2009.igem.org/Team:Newcastle/PopulationDynamics Population Dynamics model].
-Therefore, in order to ensure that sporulation occurs under the appropriate conditions, the phosphorelay must integrate the competition between signal input provided by the kinases and signal cancellation carried out by the phosphatises, which determines the decision to sporulate or not,<sup>[3][4]</sup> by governing flux through the relay and hence the level of Spo0A~P, which must reach a threshold concentration to trigger sporulation.<sup>[2]</sup>
-Other than the external and internal signals that are integrated into the phosphorelay, it is important to note that sporulation is also initiated by [https://2009.igem.org/Team:Newcastle/SporulationTuning/NutrientStarvation nutrient starvation], [https://2009.igem.org/Team:Newcastle/SporulationTuning/CellDensity cell density], and [https://2009.igem.org/Team:Newcastle/SporulationTuning/CellCycle cell cycle progression].<sup>[4]</sup>
-===KinA===
-Sporulation can be triggered with high efficiency in cells in the exponential phase of growth in rich medium by artificial induction of the synthesis of any one of three histidine kinases tha feed phosphoryl groups into the relay.<sup>[2]</sup> For our project, we will be using Kin A, a major histidine kinase responsible for activating the sporulation pathway in Bacillus subtilis.<sup>[5]</sup>
-KinA is a soluble cytoplasmic protein that appears to be active as a dimer and is composed of an amino-terminal sensor domain and a carboxy-terminal autokinase domain.<sup>[5]</sup>
-==Novelty in this sub-project==
-Instead of allowing the cell to decide whether or not to sporulate, we hope to influence it's decision. We plan to use kinA as a part of this system.
-==Modelling==
-:''See [[Team:Newcastle/Modeling/Tuning]]''
 ===KinA Expression Model===
-Under normal conditions, LacI represses KinA.
+Under normal conditions, LacI represses ''kinA''.
 [[Image:TeamNewcastleKinAExpLacIKinA.png|110px|center]]
@@ Line 56: / Line 41: @@
-However, in the presence of IPTG, KinA can be expressed, as IPTG binds to LacI, deactivating it. Equations (a) and (b) describes how IPTG binds to LacI, forming LacI*, which is the deactivated form of LacI
+However, in the presence of IPTG, KinA can be expressed, as IPTG binds to ''lacI'', deactivating it. Equations (a) and (b) describes how IPTG binds to LacI, forming LacI*, which is the deactivated form of LacI
 [[Image:TeamNewcastleKinAExpLacIIPTG1.png|220px|center]]
+:''[[Team:Newcastle/Modelling/KinAExpression#KinA_Expression_Model| Click to view more of the KinA Expression Model equations]]''
-Over time, the deactivated form of LacI, LacI* may degrade. This is also taken into consideration while building the model.
+<br>
-[[Image:TeamNewcastleKinAExpDeactivatedLacIDegradation.png|80px|center]]
-Protein synthesis requires two steps, transcription and translation, and is further illustrated in Figure 1, below.
-[[Image:TeamNewcastleKinAExpTranscriptiontranslation.png|300px|center]]
-<center>''Figure 1: Transcription and Translation''</center>
-Referring to Figure 1, the following equations can be written:
-;<u>Transcription of LacI,</u>
-[[Image:TeamNewcastleKinAExpLacITranscription.png|120px|center]]
-;<u>Translation of LacI,</u>
-[[Image:TeamNewcastleKinAExpLacITranslation.png|80px|center]]
-where mRNA_LacI is inducing the formation of LacI.
-;<u>Transcription of KinA,</u>
-[[Image:TeamNewcastleKinAExpKinATranscription.png|130px|center]]
-where LacI is repressing mRNA_KinA, therefore a lower concentration of LacI would result in a higher concentration of mRNA_KinA.
-;<u>Translation of KinA,</u>
-[[Image:TeamNewcastleKinAExpKinATranslation.png|80px|center]]
-where mRNA_KinA is inducing the formation of KinA.
 ====Results====
-The above equations were modelled in COPASI, and the following graphs show the behaviour of the system over time at different IPTG concentrations.
+[[Image:TeamNewcastleKinAExpPic1.png|center|300px]]
-;<u>IPTG concentration = 1000 nmol/fl</u>
-[[Image:TeamNewcastleKinAExpressionIptg1000.png|center|500px]]
-;<u>IPTG concentration = 3000 nmol/fl</u>
-[[Image:TeamNewcastleKinAExpressionIptg3000.png|center|500px]]
-;<u>IPTG concentration = 5000 nmol/fl</u>
-[[Image:TeamNewcastleKinAExpressionIptg5000.png|center|500px]]
-;<u>IPTG concentration = 8000 nmol/fl</u>
-[[Image:TeamNewcastleKinAExpressionIptg8000.png|center|500px]]
-;<u>IPTG concentration = 10000 nmol/fl</u>
-[[Image:TeamNewcastleKinAExpressionIptg10000.png|center|500px]]
+:''[[Team:Newcastle/Modelling/KinAExpression#Results| Click to view the KinA Expression results]]''
+<br>
 ===Sporulation Tuning Model===
-The expression of KinA has been modelled as seen above, therefore we can now proceed further into the Sporulation Tuning Model, which is built from the KinA Expression Model with COPASI.
+The expression of KinA has been modelled as seen above, therefore we can now proceed further into the Sporulation Tuning Model, which is built from the KinA Expression Model using COPASI.
-To proceed with the modelling of our Sporulation Tuning Model, we have decided that in response to an unidentified stimuli, where KinA  autophosphorylates and then donates its phosphate groups to the response regulator Spo0F, the unidentified stimuli will be termed as 'sporulation signal'.<sup>[4]</sup>
+To proceed with the modelling of our Sporulation Tuning Model, we have decided that in response to an unidentified stimulus, where KinA  autophosphorylates and then donates its phosphate groups to the response regulator Spo0F, the unidentified stimuli will be termed as 'sporulation signal'.<sup>[5]</sup>
 The following equations describe the model:
@@ Line 159: / Line 79: @@
-As Spo0F lacks an output domain and is incapable of activating transcription; it serves only as an intermediary in the phosphorelay. The phosphotransferase Spo0B transfers the phosphate from Spo0F~P to Spo0A.<sup>[4]</sup>
+:''[[Team:Newcastle/Modelling/SporulationTuning#Sporulation_Tuning_Model| Click to view more of the Sporulation Tuning Model equations]]''
-[[Image:TeamNewcastleSporeTuneEqn4.png|230px|center]]
+<br>
-<center>''Equation 4''</center>
+====Results====
-[[Image:TeamNewcastleSporeTuneEqn5.png|160px|center]]
+[[Image:TeamNewcastleSporeTunePic1.png|300px|center]]
-<center>''Equation 5''</center>
-[[Image:TeamNewcastleSporeTuneEqn6.png|280px|center]]
+:''[[Team:Newcastle/Modelling/SporulationTuning#Results| Click to view the Sporulation Tuning results]]''
-<center>''Equation 6''</center>
+<br>
-[[Image:TeamNewcastleSporeTuneEqn7.png|160px|center]]
+===Sin (sporulation inhibition) Operon Model===
-<center>''Equation 7''</center>
+In order to create a more realistic model of our sporulation system the team has decided to include the Sin (sporulation inhibition) Operon Model, which the team designed in CellML.
-[[Image:TeamNewcastleSporeTuneEqn8.png|280px|center]]
+The sin operon controls the production and activity of the repressor SinR, which in its active tetrameric form, inhibits sporulation by repressing stage II and spo0A promoters. On the other hand, the accumulation of Spo0A~P induces the expression of SinI, which binds to and inactivates SinR.
-<center>''Equation 8''</center>
+[[Image:TeamNewcastleSinOperonDiagram1.png|350px|center]]
+<center>''Diagram 1: Simplifed Schematic of the sin Operon''<sup>[9]</sup></center>
-[[Image:TeamNewcastleSporeTuneEqn9.png|160px|center]]
-<center>''Equation 9''</center>
+:''[[Team:Newcastle/Modelling/SinOperon| Click to view more of the Sin Operon Model equations]]''
-With respect to Equations 1 to 9, as seen above, the corresponding fluxes are as follows:
+<br>
-[[Image:TeamNewcastleSporeTuneFluxes2.png|200px|center]]
-<center>''Fluxes''</center>
+====Results====
-As [https://2009.igem.org/Team:Newcastle/SporulationTuning#Sporulation mentioned], the phosphotases Spo0E, YisI, and YznD dephosphorylates Spo0A, thus prevents its activation.<sup>[4]</sup>
+[[Image:TeamNewcastleSinOperonPicture1.png|200px|center]]
-===Sin (sporulation inhibition) Operon Model===
+:''[[Team:Newcastle/Modelling/SinOperon#Results| Click to view the Sin Operon Model results]]''
-[[Image:TeamNewcastleSinOperonEqn3.png|150px|center]]
-<center>''Equation 3: Transcription for P1''</center>
-[[Image:TeamNewcastleSinOperonEqn7.png|450px|center]]
+<br>
-<center>''Equation 7: Promoter Activity for P1''</center>
 ==BioBrick constructs==
-The BioBrick we have designed is to contain an IPTG inducable kinA gene, using pSpac, allowing us to test the theory about KinA in the lab.
+The BioBrick we have designed is to contain an IPTG inducable ''kinA'' gene, using pSpac, allowing us to test the theory about KinA in the lab.
 '''BBa_K174010'''
@@ Line 228: / Line 142: @@
 ==Lab Work Strategies==
-The lab work will mainly be to test our BioBrick using IPTG.
-==Other Presentations and Diagrams==
+The lab work executed was be to induce sporulation in the presence of IPTG, and this involved microscopy and testing cultures for sporulation (e.g. by their heat resistance).
+[[Image:Newcastle KinA-sporulation1.JPG|center|400px]]
+To find out more about our lab work strategies,
+:''see [[Team:Newcastle/SporulationTuning/Lab_Work_Strategies| Lab Work Strategies]]''
 ==References==
-[1] Veening, J-W., Smits, W. K., Kuipers, O. P. (2008) Bistability, Epigenetics, and Bet-Hedging in Bacteria. Annu. Rev. Microbiol. 62: 193-210
+[1] Predich, M., Nair, G., Smith, I. (1992) ''Bacillus subtilis'' Early Sporulation Genes ''kinA'', ''spo0F'', and ''spo0A'' Are Transcribed by the RNA Polymerase Containing σ<sup>H</sup>. Journal of Bacteriology. Pp 2771-2778
+[2] Veening, J-W., Smits, W. K., Kuipers, O. P. (2008) Bistability, Epigenetics, and Bet-Hedging in Bacteria. Annu. Rev. Microbiol. 62: 193-210
+[3] Fujita, M., Losick, R. (2005) Evidence that Entry into Sporulation in Bacillus subtilis is Governed by a Gradual Increase in the Level and Activity of the Master Regulator Spo0A. 19: 2236–2244
+[4] Sonenshein, A.L., Hoch, J.A., Losick, R., (2002) Bacillus subtilis and Its Closest Relatives From Genes to Cells. ASM Press, United States of America. Pp 476–477
+[5] Hilbert, D.W., Piggot, P.J., (June 2004) Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation. Microbiology and Molecular Biology Reviews. Vol. 68, No. 2. Pp 234-262
-[2] Fujita, M., Losick, R. (2005) Evidence that Entry into Sporulation in Bacillus subtilis is Governed by a Gradual Increase in the Level and Activity of the Master Regulator Spo0A. 19: 2236–2244
+[6] Eswaramoorthy, P., Guo, T., Fujita, M. (2009) In Vivo Domain-Based Functional Analysis of the Major Sporulation Sensor Kinase, KinA, in Bacillus subtilis. Journal of Bacteriology. Pp 5358-5368
-[3] Sonenshein, A.L., Hoch, J.A., Losick, R., (2002) Bacillus subtilis and Its Closest Relatives From Genes to Cells. ASM Press, United States of America. Pp 476–477
+[7] Stephenson, K., Hoch, J. A. (2001) PAS-A domain of phosphorelay sensor kinase A: A catalytic ATP-binding domain involved in the initiation of development in ''Bacillus subtilis''. PNAS. Vol. 98, no. 26: 15251-15256
-[4] Hilbert, D.W., Piggot, P.J., (June 2004) Compartmentalization of Gene Expression during Bacillus subtilis Spore Formation. Microbiology and Molecular Biology Reviews. Vol. 68, No. 2. Pp 234-262
+[8] Veening, J-W., Hamoen, L. W., Kuipers, O. P. (2005) Phosphatases modulate the bistable sporulation gene expression pattern in ''Bacillus subtilis''. Molecular Microbiology 56(6), 1481-1494
-[5] Eswaramoorthy, P., Guo, T., Fujita, M. (2009) In Vivo Domain-Based Functional Analysis of the Major Sporulation Sensor Kinase, KinA, in Bacillus subtilis. Journal of Bacteriology. Pp 5358-5368
+[9] Voigt, C. A., Wolf, D. M., Arkin, A. P. (2004) The ''Bacillus subtilis sin'' Operon: An Evolvable Network Motif. Genetics 169: 1187-1202
-{{:Team:Newcastle/Footer}}
+<br>
-{{:Team:Newcastle/Right}}