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Team:Groningen/Project/Motility
From 2013.igem.org
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| - | < | + | <h1>Stay Warm, Stay Close</h1> |
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| - | Our initial idea was to let the bacteria produce the silk in a bath and when the implant is put into the bath, the implant will be coated with silk. This is a wasteful and inelegant method. A low production yield can be expected and a solution is needed to overcome this problem. Therefore the heat motility was developed. With the help of heat motility the silk will be produced on site, this will also save energy in the form of nutrition and energy of heating the bath. | + | Our initial idea was to let the bacteria produce the silk in a bath and when the implant is put into the bath, the implant will be coated with silk. This is a wasteful and inelegant method. A low production yield can be expected and a solution is needed to overcome this problem. Therefore the heat motility was developed. With the help of heat motility the silk will be produced on site, this will also save energy in the form of nutrition and energy of heating the bath. An overview of our 'Coating GEM' is shown in figure 1. |
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<h2>Native Motility</h2> | <h2>Native Motility</h2> | ||
<p> | <p> | ||
| - | The Motility in most bacteria is governed by the | + | The Motility in most bacteria is governed by the Che proteins [1], they control if the bacteria is swimming straight or tumbling (changing directions). They do this by controlling the flagella. If the flagella spin counter-clockwise (CCW) they will group together in one pole of the bacterium, causing straight swimming. On the other hand if the flagella are spinning clockwise (CW) then the flagella will disperse over the membrane and cause tumbling. |
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<h3>CheY</h3> | <h3>CheY</h3> | ||
| - | The Che proteins are present in many motile bacteria, however they can have different effects depending on the species. The CheY protein in <i>Bacillus subtilis</i>, for example, has the complete opposite effect as in <i>Escherichia coli</i>. CheY is an important protein for controlling the spinning of the flagella. When the concentration of phosphorylated CheY (CheY-p) is sufficiently high the flagella turn CCW (straight swimming), but when the concentration of CheY decreases the chance of tumbling also increases, and the bacterium will reorient themselves more often. | + | The Che proteins are present in many motile bacteria, however they can have different effects depending on the species [1]. The CheY protein in <i>Bacillus subtilis</i>, for example, has the complete opposite effect as in <i>Escherichia coli</i>. CheY is an important protein for controlling the spinning of the flagella. When the concentration of phosphorylated CheY (CheY-p) is sufficiently high the flagella turn CCW (straight swimming), but when the concentration of CheY decreases the chance of tumbling also increases, and the bacterium will reorient themselves more often. |
</p> | </p> | ||
<h3>Attractant Receptor</h3> | <h3>Attractant Receptor</h3> | ||
<p> | <p> | ||
| - | The chemotaxis process is initiated at the receptor, which can sense the concentration of an attractant (or repellent). Increasing concentrations of attractant correspond to an increased chance of swimming. If the concentration decreases, the bacteria will start to tumble more frequently, and will reorient its swimming direction, hopefully to more desirable regions. | + | The chemotaxis process is initiated at the receptor, which can sense the concentration of an attractant (or repellent) [2]. Increasing concentrations of attractant correspond to an increased chance of swimming. If the concentration decreases, the bacteria will start to tumble more frequently, and will reorient its swimming direction, hopefully to more desirable regions. |
</p> | </p> | ||
<h3>cheA & CheC-CheD</h3> | <h3>cheA & CheC-CheD</h3> | ||
| - | Binding of the attractant receptor causes straight swimming via a small cascade. When the receptor is bound, the CheA protein (which is attached to it) gets phosphorylated. The CheA-p phophorylates cheY, which then causes straight swimming. The protein complex CheC-CheD causes dephophorylation of cheY-p (when receptor is bound) resulting in a negative feedback. Two more negative feedback systems are also activated following the binding of attractant, which also result in decreased values of CheY-p. In such a way, CheY-p adaption occurs, and <i>B. subtilis</i> is ready to sense new changes in its environment. For more information about how this pathway works please visit <a href="https://2013.igem.org/Team:Groningen/Navigation/Heatmotility#six"> | + | Binding of the attractant receptor causes straight swimming via a small cascade [2]. When the receptor is bound, the CheA protein (which is attached to it) gets phosphorylated. The CheA-p phophorylates cheY, which then causes straight swimming. The protein complex CheC-CheD causes dephophorylation of cheY-p (when receptor is bound) resulting in a negative feedback. Two more negative feedback systems are also activated following the binding of attractant, which also result in decreased values of CheY-p. In such a way, CheY-p adaption occurs, and <i>B. subtilis</i> is ready to sense new changes in its environment. For more information about how this pathway works please visit the <a href="https://2013.igem.org/Team:Groningen/Navigation/Heatmotility#six">heat motility section</a>. |
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| - | <font size="1">Figure 1: | + | <font size="1">Figure 1: The scheme shows <i>B. subtilis</i> containing knockouts of <i>cheY</i>, <i>cheC</i> and <i>des</i>. It also shows the motility gene and the silk gene positively controlled by cold and heat respectively. </font> |
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<h3 id = "special"><i>cheY</i> Knockout</h3> | <h3 id = "special"><i>cheY</i> Knockout</h3> | ||
<p> | <p> | ||
| - | To make our coating mechanism a success we need to have control over the motility. This is achieved by knocking out <i>cheY</i>. This might sound strange since CheY-p is controlling straight swimming. However since we know that a CheY null mutant is immobile due to excessive tumbling. This makes it possible to insert <i>cheY</i> with a promoter of our choosing, and make it the sole producer of CheY. How this is effecting the cell is explained in more detail with our <a href="https://2013.igem.org/Team:Groningen/Navigation/Heatmotility#six">model</a>. | + | To make our coating mechanism a success we need to have control over the motility. This is achieved by knocking out <i>cheY</i>. This might sound strange since CheY-p is controlling straight swimming. However since we know that a CheY null mutant is immobile due to excessive tumbling. This makes it possible to insert <i>cheY</i> with a promoter of our choosing, and make it the sole producer of CheY. Also a <i>cheC</i> knockout is made in order to prevent negative feedback. How this is effecting the cell is explained in more detail with our <a href="https://2013.igem.org/Team:Groningen/Navigation/Heatmotility#six">model</a>. |
</p> | </p> | ||
<h3>DesK pathway</h3> | <h3>DesK pathway</h3> | ||
<p> | <p> | ||
| - | We envision a bacterium that moves towards a heat source, in order to do this it needs a temperature sensor. <i>B. subtilis</i> natively has a protein that fits this requirement nicely. It is called DesK, it is a membrane protein that senses cold (25°C). When the environment is cold, DesK autophophorylates, after which it phosphorylates DesR. DesR in turn activates the promoter of the des gene (P<sub><i>des</i></sub>), which would be the promoter we are looking for. The <i>des</i> gene expresses a protein that provides negative feedback to the system, so we need to knockout this des gene to keep our promoter active. | + | We envision a bacterium that moves towards a heat source, in order to do this it needs a temperature sensor. <i>B. subtilis</i> natively has a protein that fits this requirement nicely. It is called DesK, it is a membrane protein that senses cold [3][4] (25°C). When the environment is cold, DesK autophophorylates, after which it phosphorylates DesR. DesR in turn activates the promoter of the des gene (P<sub><i>des</i></sub>), which would be the promoter we are looking for. The <i>des</i> gene expresses a protein that provides negative feedback to the system, so we need to knockout this des gene to keep our promoter active. |
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<h3>Thermal control of fatty acid synthesis.</h3> | <h3>Thermal control of fatty acid synthesis.</h3> | ||
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| - | The desaturation of the membrane starts with the membrane protein, DesK. DesK senses temperature of its environment and when the temperature is | + | The desaturation of the membrane starts with the membrane protein, DesK. DesK senses temperature of its environment and when the temperature is 30°C, DesK autophosphorylates its conserved histidine. Sequentially the phosphoryl group is transferred to the aspartate residue in desR that activates the promoter of <i>des</i>. The gene <i>des</i> is translated into a fatty acid desaturase (Δ5-Des), that changes the fluidity of the membrane by introducing |
double bonds into pre-existing saturated fatty acyl chains. | double bonds into pre-existing saturated fatty acyl chains. | ||
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| - | <font size="1">Figure 2: Pattern of P<i>des</i>-<i>lacZ</i> expression on a temperature downshift.</b>(a) <i>B. subtilis</i> AKP3 cells were grown at 37 °C to an optical density of 0.4 at 525 nm and then divided into two fractions. The first was transferred to 25 °C (●) and the second was kept at 37 °C (○). (b) Pattern of P<i>des</i>-<i>lacZ</i> expression in a <i>des</i>‾ background. <i>B. subtilis</i> AKP4 cells were grown at 37 °C to an optical density of 0.4 at 525 nm and then divided into two fractions. One fraction was transferred to 25 °C (●) while the other was kept at 37 °C (○). (c). Effect of exogenous fatty acids on P<i>des</i>-<i>lacZ</i> expression pattern. <i>B. subtilis</i> AKP4 cells were grown at 37 °C to an optical density of 0.4 at 525 nm and then divided into two fractions. Each fraction was supplemented with palmitic (●) or oleic acid (■) and growth was continued at 25 °C. (d) Effect of <i>desKR</i> disruption on P<i>des</i>-<i>lacZ</i> expression. <i>B. subtilis</i> AKP21 cells were grown at 37 °C to an optical density of 0.4 at 525 nm and then divided into two fractions. One of the fractions was transferred to 25 °C (●) and the other one was kept at 37 °C (○). Optical density at 525 nm (inserts) and β-galactosidase specific activity were determined at the indicated times (a, b, c, or d). </font> | + | <font size="1">Figure 2: Pattern of P<i>des</i>-<i>lacZ</i> expression on a temperature downshift.</b>(a) <i>B. subtilis</i> AKP3 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. The first was transferred to 25°C (●) and the second was kept at 37°C (○). (b) Pattern of P<i>des</i>-<i>lacZ</i> expression in a <i>des</i>‾ background. <i>B. subtilis</i> AKP4 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. One fraction was transferred to 25°C (●) while the other was kept at 37°C (○). (c). Effect of exogenous fatty acids on P<i>des</i>-<i>lacZ</i> expression pattern. <i>B. subtilis</i> AKP4 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. Each fraction was supplemented with palmitic (●) or oleic acid (■) and growth was continued at 25°C. (d) Effect of <i>desKR</i> disruption on P<i>des</i>-<i>lacZ</i> expression. <i>B. subtilis</i> AKP21 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. One of the fractions was transferred to 25°C (●) and the other one was kept at 37°C (○). Optical density at 525 nm (inserts) and β-galactosidase specific activity were determined at the indicated times (a, b, c, or d). </font> |
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<h2>Motility</h2> | <h2>Motility</h2> | ||
<h3>The principle</h3> | <h3>The principle</h3> | ||
| - | CheY is a mayor factor in spinning the flagella CCW. When <i>cheY</i> is absent, cells are significant less motile[ref]. Because the promoter of <i>des</i> is active at low temperatures (25 °C) we placed <i>cheY</i> under control of the promoter of <i>des</i> (figure 2). | + | CheY is a mayor factor in spinning the flagella CCW. When <i>cheY</i> is absent, cells are significant less motile[ref]. Because the promoter of <i>des</i> is active at low temperatures (25°C) we placed <i>cheY</i> under control of the promoter of <i>des</i> (figure 2). |
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<h2>The coating</h2> | <h2>The coating</h2> | ||
| - | The silk proteins are secreted with a Strep tag. The implant will be covered with biotin (vitamine B8). The Strep tag will automatically form a Van der Waals binding with the biotin and thus, if the silk is secreted closely the implant will be coated automatically. B.subtilis has a tendency to form a biofilm on a structure, or in our case an implant (insert proof that biofilm can grow in plastic/titanium) . To coat the implant we have thought of to option 1 via secretion and 2 via a biofilm formation. The secretion process is the most elegant and best option, but secretion of large proteins is proven to be difficult and has never been done before with silk. So a ‘backup’ plan was needed. | + | The silk proteins are secreted with a Strep tag. The implant will be covered with biotin (vitamine B8). The Strep tag will automatically form a Van der Waals binding with the biotin and thus, if the silk is secreted closely the implant will be coated automatically. <i>B.subtilis</i> has a tendency to form a biofilm on a structure, or in our case an implant (insert proof that biofilm can grow in plastic/titanium) . To coat the implant we have thought of to option 1 via secretion and 2 via a biofilm formation. The secretion process is the most elegant and best option, but secretion of large proteins is proven to be difficult and has never been done before with silk. So a ‘backup’ plan was needed. |
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<h2>References</h2> | <h2>References</h2> | ||
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| - | [1] | + | [1] Liam F. Garrity and George W. Ordal, Chemotaxis in <i>Bacillus subtilis</i>: How bacteria monitor environmental signals, <i>Pharmacology and Therepeutics</i> (1995), Vol. 68 No.1, pp. 87-104. |
<br>[2] Christopher V. Rao, George D. Glekas and George W. Ordal, The three adaptation systems of <i>Bacillus subtilis</i> chemotaxis, <i>Trends in Biology</i> (2008), Vol. 16 No 10, pp. 480-487. | <br>[2] Christopher V. Rao, George D. Glekas and George W. Ordal, The three adaptation systems of <i>Bacillus subtilis</i> chemotaxis, <i>Trends in Biology</i> (2008), Vol. 16 No 10, pp. 480-487. | ||
| - | <br>[3] | + | <br>[3] Mariana Martin and Diego de Mendoza, Regulation of <i>Bacillus subtilis</i> DesK thermosensor by lipids, <i>Biochemical Journal</i> (2013), Vol 451 No 2, pp. 269–275. |
<br>[4] Thermal Regulation of Membrane Lipid Fluidity by a Two-Component System in <i>Bacillus subtilis</i>, January 31 2011, BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Vol. 39, No. 5, pp. 362–366, 2011. | <br>[4] Thermal Regulation of Membrane Lipid Fluidity by a Two-Component System in <i>Bacillus subtilis</i>, January 31 2011, BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Vol. 39, No. 5, pp. 362–366, 2011. | ||
</p> | </p> | ||
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</html> | </html> | ||
Latest revision as of 03:53, 5 October 2013
Stay Warm, Stay Close
Our initial idea was to let the bacteria produce the silk in a bath and when the implant is put into the bath, the implant will be coated with silk. This is a wasteful and inelegant method. A low production yield can be expected and a solution is needed to overcome this problem. Therefore the heat motility was developed. With the help of heat motility the silk will be produced on site, this will also save energy in the form of nutrition and energy of heating the bath. An overview of our 'Coating GEM' is shown in figure 1.
Native Motility
The Motility in most bacteria is governed by the Che proteins [1], they control if the bacteria is swimming straight or tumbling (changing directions). They do this by controlling the flagella. If the flagella spin counter-clockwise (CCW) they will group together in one pole of the bacterium, causing straight swimming. On the other hand if the flagella are spinning clockwise (CW) then the flagella will disperse over the membrane and cause tumbling.
CheY
The Che proteins are present in many motile bacteria, however they can have different effects depending on the species [1]. The CheY protein in Bacillus subtilis, for example, has the complete opposite effect as in Escherichia coli. CheY is an important protein for controlling the spinning of the flagella. When the concentration of phosphorylated CheY (CheY-p) is sufficiently high the flagella turn CCW (straight swimming), but when the concentration of CheY decreases the chance of tumbling also increases, and the bacterium will reorient themselves more often.Attractant Receptor
The chemotaxis process is initiated at the receptor, which can sense the concentration of an attractant (or repellent) [2]. Increasing concentrations of attractant correspond to an increased chance of swimming. If the concentration decreases, the bacteria will start to tumble more frequently, and will reorient its swimming direction, hopefully to more desirable regions.
cheA & CheC-CheD
Binding of the attractant receptor causes straight swimming via a small cascade [2]. When the receptor is bound, the CheA protein (which is attached to it) gets phosphorylated. The CheA-p phophorylates cheY, which then causes straight swimming. The protein complex CheC-CheD causes dephophorylation of cheY-p (when receptor is bound) resulting in a negative feedback. Two more negative feedback systems are also activated following the binding of attractant, which also result in decreased values of CheY-p. In such a way, CheY-p adaption occurs, and B. subtilis is ready to sense new changes in its environment. For more information about how this pathway works please visit the heat motility section.
|
| Figure 1: The scheme shows B. subtilis containing knockouts of cheY, cheC and des. It also shows the motility gene and the silk gene positively controlled by cold and heat respectively. |
Controllable motility
cheY Knockout
To make our coating mechanism a success we need to have control over the motility. This is achieved by knocking out cheY. This might sound strange since CheY-p is controlling straight swimming. However since we know that a CheY null mutant is immobile due to excessive tumbling. This makes it possible to insert cheY with a promoter of our choosing, and make it the sole producer of CheY. Also a cheC knockout is made in order to prevent negative feedback. How this is effecting the cell is explained in more detail with our model.
DesK pathway
We envision a bacterium that moves towards a heat source, in order to do this it needs a temperature sensor. B. subtilis natively has a protein that fits this requirement nicely. It is called DesK, it is a membrane protein that senses cold [3][4] (25°C). When the environment is cold, DesK autophophorylates, after which it phosphorylates DesR. DesR in turn activates the promoter of the des gene (Pdes), which would be the promoter we are looking for. The des gene expresses a protein that provides negative feedback to the system, so we need to knockout this des gene to keep our promoter active.
Thermal control of fatty acid synthesis.
In order to maintain the fluidity of the cell membrane when the environmental temperature is decreasing, B. subtilis (among other bacteria) adapts the membrane by increasing the fraction of unsaturated phospholipids acyl chains.
The desaturation of the membrane starts with the membrane protein, DesK. DesK senses temperature of its environment and when the temperature is 30°C, DesK autophosphorylates its conserved histidine. Sequentially the phosphoryl group is transferred to the aspartate residue in desR that activates the promoter of des. The gene des is translated into a fatty acid desaturase (Δ5-Des), that changes the fluidity of the membrane by introducing double bonds into pre-existing saturated fatty acyl chains.
The promoter activity of des
|
| Figure 2: Pattern of Pdes-lacZ expression on a temperature downshift.(a) B. subtilis AKP3 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. The first was transferred to 25°C (●) and the second was kept at 37°C (○). (b) Pattern of Pdes-lacZ expression in a des‾ background. B. subtilis AKP4 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. One fraction was transferred to 25°C (●) while the other was kept at 37°C (○). (c). Effect of exogenous fatty acids on Pdes-lacZ expression pattern. B. subtilis AKP4 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. Each fraction was supplemented with palmitic (●) or oleic acid (■) and growth was continued at 25°C. (d) Effect of desKR disruption on Pdes-lacZ expression. B. subtilis AKP21 cells were grown at 37°C to an optical density of 0.4 at 525 nm and then divided into two fractions. One of the fractions was transferred to 25°C (●) and the other one was kept at 37°C (○). Optical density at 525 nm (inserts) and β-galactosidase specific activity were determined at the indicated times (a, b, c, or d). |
| Strain | Description |
|---|---|
| JH642 | trpC2 pheA1 |
| AKP3 | JH642 amyE::[Pdes(-2269 to +31)lacZ] |
| AKP4 | AKP3 des::kan |
| AKP21 | AKP3 desKR::kan |
The coating
The silk proteins are secreted with a Strep tag. The implant will be covered with biotin (vitamine B8). The Strep tag will automatically form a Van der Waals binding with the biotin and thus, if the silk is secreted closely the implant will be coated automatically. B.subtilis has a tendency to form a biofilm on a structure, or in our case an implant (insert proof that biofilm can grow in plastic/titanium) . To coat the implant we have thought of to option 1 via secretion and 2 via a biofilm formation. The secretion process is the most elegant and best option, but secretion of large proteins is proven to be difficult and has never been done before with silk. So a ‘backup’ plan was needed.Animation
Motility of the knockout strains
To observe whether or not the mutant strains are less motile than the wild type strain different tests are done. One of the tests is performed using microscopy.Microscope movies
Microscope movies (4x real time) are made for the wildtype, the ΔcheY and the ΔcheYΔdes strain. These movies show that the wildtype strain (Movie 1) is more motile than both mutant strains. The comparison between the movie of the ΔcheY (Movie 2) and ΔcheYΔdes (Movie 3) strain shows just as seen in the motility assay, that the ΔcheYΔdes strain is less motile than the ΔcheY strain.Movie 1: Motility of the wild type strain
Movie 2: Motility of ΔcheY
Movie 3: Motility of ΔcheYΔdes
References
[1] Liam F. Garrity and George W. Ordal, Chemotaxis in Bacillus subtilis: How bacteria monitor environmental signals, Pharmacology and Therepeutics (1995), Vol. 68 No.1, pp. 87-104.
[2] Christopher V. Rao, George D. Glekas and George W. Ordal, The three adaptation systems of Bacillus subtilis chemotaxis, Trends in Biology (2008), Vol. 16 No 10, pp. 480-487.
[3] Mariana Martin and Diego de Mendoza, Regulation of Bacillus subtilis DesK thermosensor by lipids, Biochemical Journal (2013), Vol 451 No 2, pp. 269–275.
[4] Thermal Regulation of Membrane Lipid Fluidity by a Two-Component System in Bacillus subtilis, January 31 2011, BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Vol. 39, No. 5, pp. 362–366, 2011.
