Team:Groningen/Project/Vesicle

From 2009.igem.org

(Difference between revisions)
(Cloning strategy)
m
Line 9: Line 9:
Gas vesicles are hollow proteinous organelles made of gvpA and gvpC (in cyanobacteria) and are permeable to gases and fills by diffusion. It is impermeable to water because of its hydrophobic inside. GvpA is a small 70AA long protein which forms a linear crystalline array of ribs to form the cylindrical shell and conical ends. GvpC is usually on the outside of the gas vesicle to make it stronger and stabilizes the structure (see Figure 1).
Gas vesicles are hollow proteinous organelles made of gvpA and gvpC (in cyanobacteria) and are permeable to gases and fills by diffusion. It is impermeable to water because of its hydrophobic inside. GvpA is a small 70AA long protein which forms a linear crystalline array of ribs to form the cylindrical shell and conical ends. GvpC is usually on the outside of the gas vesicle to make it stronger and stabilizes the structure (see Figure 1).
-
In ''B. megaterium'' a gas vesicle gene-cluster was found, which contained 14 gvp genes (gas vescicle polycitonic genes) which were functionally expressed in ''<i>E. coli</i>'' by Ning Li and Maura Cannon [[Team:Groningen/Literature#Li1998 |Li1998]]. The best bouyant fenotype was found when  gvpA, gvpP, gvpQ and ORF-1 were excluded (see figure 2). It was suggested that gvpB on the gvp-cluster of B. megaterium is an homolog of gvpA.
+
In ''B. megaterium'' a gas vesicle gene-cluster was found, which contained 14 gvp genes (gas vescicle polycitonic genes) which were functionally expressed in <i>E. coli</i> by Ning Li and Maura Cannon ([[Team:Groningen/Literature#Li1998|Li 1998]]). The best bouyant fenotype was found when  gvpA, gvpP, gvpQ and ORF-1 were excluded (see figure 2). It was suggested that gvpB on the gvp-cluster of <i>B. megaterium</i> is an homolog of gvpA.
==Gas vesicles in iGEM==
==Gas vesicles in iGEM==
Line 20: Line 20:
[http://parts.mit.edu/igem07/index.php/Melbourne/Lab_GV_Notebook Melbourne iGEM 2007 team] constructed a bouyant <i>E. coli</i> and also they added a <partinfo>BBa_I750016</partinfo> of the short version of the gvp-cluster (without gvpA,P,Q, ORF-1 and AraC). This BioBrick is available and also in the microtiter plate send by HQ to us, so we can use this. Melbourne changed the gvp-cluster by cleaning it from 3 ''Eco''RI sites and 1 ''Pst''I site, this leaded to a accidental addition of a 10x repeat of "TCTGCAAATTA". They mention that they added the BioBrick prefix and suffix to the BioBrick, though the restriction sites of these additions cannot be found by CloneManager in the sequence available on the Partregistry. Hopefully the part is available on a standard vector, which has the pre- and suffix for BioBricks. For cloning this part we can use the [http://parts.mit.edu/igem07/index.php/Melbourne/Lab_Notebook_gv_6 optimized protocol ] (restriction on part with ''Xba''I and ''Spe''I, on the vector with ''Spe''I) for ligation of the gvp-cluster and a {{part|BBa_J61035|vector BBa_J61035}} (3539bp, copy nr??), this unluckily leads to ligation of the gvp-cluster in an unspecific direction. This can of course be tested by restriction, PCR or sequencing, but it takes more time as another step will be introduced. The vector has two selection markers: Ampicillin and Gentamycin.
[http://parts.mit.edu/igem07/index.php/Melbourne/Lab_GV_Notebook Melbourne iGEM 2007 team] constructed a bouyant <i>E. coli</i> and also they added a <partinfo>BBa_I750016</partinfo> of the short version of the gvp-cluster (without gvpA,P,Q, ORF-1 and AraC). This BioBrick is available and also in the microtiter plate send by HQ to us, so we can use this. Melbourne changed the gvp-cluster by cleaning it from 3 ''Eco''RI sites and 1 ''Pst''I site, this leaded to a accidental addition of a 10x repeat of "TCTGCAAATTA". They mention that they added the BioBrick prefix and suffix to the BioBrick, though the restriction sites of these additions cannot be found by CloneManager in the sequence available on the Partregistry. Hopefully the part is available on a standard vector, which has the pre- and suffix for BioBricks. For cloning this part we can use the [http://parts.mit.edu/igem07/index.php/Melbourne/Lab_Notebook_gv_6 optimized protocol ] (restriction on part with ''Xba''I and ''Spe''I, on the vector with ''Spe''I) for ligation of the gvp-cluster and a {{part|BBa_J61035|vector BBa_J61035}} (3539bp, copy nr??), this unluckily leads to ligation of the gvp-cluster in an unspecific direction. This can of course be tested by restriction, PCR or sequencing, but it takes more time as another step will be introduced. The vector has two selection markers: Ampicillin and Gentamycin.
-
 
-
==Alternative cloning strategy==
 
-
Another possibility is to use eg. ''Xba''I and ''Spe''I and also cut a vector with these enzymes, this would lead to ligation of the gvp-cluster in one direction. A possible vector for this strategy on the partsregistry is: {{part|BBa_J23018}} (2298 bp).
 
Line 29: Line 26:
To create a floating device, we will use the biobrick gas vesicle cluster (GVP), it will be tryed to improve this biobrick by removing the 11x repeat. The GVP cluster will be expressed under control of a metal sensitive promoter.
To create a floating device, we will use the biobrick gas vesicle cluster (GVP), it will be tryed to improve this biobrick by removing the 11x repeat. The GVP cluster will be expressed under control of a metal sensitive promoter.
 +
 +
===Alternative cloning strategy===
 +
Another possibility is to use eg. ''Xba''I and ''Spe''I and also cut a vector with these enzymes, this would lead to ligation of the gvp-cluster in one direction. A possible vector for this strategy on the partsregistry is: {{part|BBa_J23018}} (2298 bp).
 +
==Modelling==
==Modelling==
 +
===Buoyancy===
===Buoyancy===
-
The gas vesicles are shaped roughly like a cylinder with a cone at each end, whose cross-section we model as (based mostly on [[Team:Groningen/Literature#Walsby1994|Walsby1994]]):
+
The gas vesicles are shaped roughly like a cylinder with a cone at each end, whose cross-section we model as (based mostly on [[Team:Groningen/Literature#Walsby1994|Walsby 1994]]):
[[Image:Vesicle_Shape.png]]
[[Image:Vesicle_Shape.png]]
-
We assume the interior of the wall of the gas vesicle is similarly shaped to the exterior, just slightly smaller (the right-most part of the image above illustrates this situation for the left tip of the gas vesicle). This means the different dimensions are related through the equations below. To determine the total volume, just use them with the given width/diameter (at least for the dimensions given in [[Team:Groningen/Literature#Walsby1994|Walsby1994]]). To determine the gas volume, use them with w<sub>gas</sub> and d<sub>gas</sub>.
+
We assume the interior of the wall of the gas vesicle is similarly shaped to the exterior, just slightly smaller (the right-most part of the image above illustrates this situation for the left tip of the gas vesicle). This means the different dimensions are related through the equations below. To determine the total volume, just use them with the given width/diameter (at least for the dimensions given in [[Team:Groningen/Literature#Walsby1994|Walsby 1994]]). To determine the gas volume, use them with w<sub>gas</sub> and d<sub>gas</sub>.
{|
{|
Line 247: Line 249:
'''Explanation of the graph'''
'''Explanation of the graph'''
-
Three curves are shown, corresponding to how many gas vesicles a cell needs with "our" gas vesicles (unless you changed the constants in the calculator above), the gas vesicles documented in [[Team:Groningen/Literature#Li1998|Li1998]]{{infoBox|Using a width and diameter of 75nm and 50nm, respectively. Here we assume that their "width" should be interpreted as our diameter, as doing it the other way around would leave no room for a cylinder and they specifically mention that the vesicles appear to be shaped like cylinders with conical ends.}} and the gas vesicles from Anabaena in [[Team:Groningen/Literature#Walsby1994|Walsby1994]]{{infoBox|Using a width and diameter of 500nm and 84nm, respectively.}}.
+
Three curves are shown, corresponding to how many gas vesicles a cell needs with "our" gas vesicles (unless you changed the constants in the calculator above), the gas vesicles documented in [[Team:Groningen/Literature#Li1998|Li 1998]]{{infoBox|Using a width and diameter of 75nm and 50nm, respectively. Here we assume that their "width" should be interpreted as our diameter, as doing it the other way around would leave no room for a cylinder and they specifically mention that the vesicles appear to be shaped like cylinders with conical ends.}} and the gas vesicles from Anabaena in [[Team:Groningen/Literature#Walsby1994|Walsby 1994]]{{infoBox|Using a width and diameter of 500nm and 84nm, respectively.}}.
'''The X-axis''' depicts the cell density of the part of the cell not occupied by gas vesicles.
'''The X-axis''' depicts the cell density of the part of the cell not occupied by gas vesicles.
Line 269: Line 271:
** (How fast are they produced?)
** (How fast are they produced?)
-
-Cyanobacteria [[Team:Groningen/Literature#Bowen1965|Bowen1965]]: gas vacuoles made up of gas vesicles (75 nm in diameter and up to 1.0 ,um in length, single wall layer only 2 nm thick) 0,7MPa gives irreversible loss of buoyancy fenotype, but found in next generation.
+
-Cyanobacteria [[Team:Groningen/Literature#Bowen1965|Bowen 1965]]: gas vacuoles made up of gas vesicles (75 nm in diameter and up to 1.0 ,um in length, single wall layer only 2 nm thick) 0,7MPa gives irreversible loss of buoyancy fenotype, but found in next generation.
-
you can use a nephelometer, to measurement the light scattering of the gas vesicles [[Team:Groningen/Literature#walsby1994|Walsby1994]]
+
you can use a nephelometer, to measurement the light scattering of the gas vesicles ([[Team:Groningen/Literature#walsby1994|Walsby 1994]])
-
=='''Planning and requirements:'''==
+
==Planning and requirements:==
*'''Modelling:'''
*'''Modelling:'''

Revision as of 20:59, 10 October 2009

Igemhomelogo.png


Introduction

About 150 species of prokaryotes (well studied examples are cyanobacteria and halophilic archaea) in aquatic habitats have been shown to contain gas vesicles. These gas vesicles provide cells with bouyancy, there function is either to positioning the bacterium (in water) in order to get the right amount of oxygen or the right amount of light. Gas vesicles are made exclusively of proteins and contain gas. When gas vesicles are present in a cell, the overall density of that cell is lowered and the cell becomes bouyant.

We want to utilize this bouyancy for an application like for example separation of specific molecules or specific cells.

Gas vesicles are hollow proteinous organelles made of gvpA and gvpC (in cyanobacteria) and are permeable to gases and fills by diffusion. It is impermeable to water because of its hydrophobic inside. GvpA is a small 70AA long protein which forms a linear crystalline array of ribs to form the cylindrical shell and conical ends. GvpC is usually on the outside of the gas vesicle to make it stronger and stabilizes the structure (see Figure 1).

In B. megaterium a gas vesicle gene-cluster was found, which contained 14 gvp genes (gas vescicle polycitonic genes) which were functionally expressed in E. coli by Ning Li and Maura Cannon (Li 1998). The best bouyant fenotype was found when gvpA, gvpP, gvpQ and ORF-1 were excluded (see figure 2). It was suggested that gvpB on the gvp-cluster of B. megaterium is an homolog of gvpA.

Gas vesicles in iGEM

In iGEM 2007, Melbourne created a biobrick for gas vesicle formation. In iGEM 2008 Kyoto had the idea to lift the titanic from the bottom of the sea with the help of bouyant bacteria.

Figure 1: Gas vesicle cluster ()


Melbourne iGEM 2007 team constructed a bouyant E. coli and also they added a of the short version of the gvp-cluster (without gvpA,P,Q, ORF-1 and AraC). This BioBrick is available and also in the microtiter plate send by HQ to us, so we can use this. Melbourne changed the gvp-cluster by cleaning it from 3 EcoRI sites and 1 PstI site, this leaded to a accidental addition of a 10x repeat of "TCTGCAAATTA". They mention that they added the BioBrick prefix and suffix to the BioBrick, though the restriction sites of these additions cannot be found by CloneManager in the sequence available on the Partregistry. Hopefully the part is available on a standard vector, which has the pre- and suffix for BioBricks. For cloning this part we can use the optimized protocol (restriction on part with XbaI and SpeI, on the vector with SpeI) for ligation of the gvp-cluster and a vector BBa_J61035 (3539bp, copy nr??), this unluckily leads to ligation of the gvp-cluster in an unspecific direction. This can of course be tested by restriction, PCR or sequencing, but it takes more time as another step will be introduced. The vector has two selection markers: Ampicillin and Gentamycin.


Cloning strategy

figure 2: The floating device will be built up of an inducible promoter which can be induced by a certain intracellular concentration of metal-ions, and a gas vesicle cluster.

To create a floating device, we will use the biobrick gas vesicle cluster (GVP), it will be tryed to improve this biobrick by removing the 11x repeat. The GVP cluster will be expressed under control of a metal sensitive promoter.

Alternative cloning strategy

Another possibility is to use eg. XbaI and SpeI and also cut a vector with these enzymes, this would lead to ligation of the gvp-cluster in one direction. A possible vector for this strategy on the partsregistry is: BBa_J23018 (2298 bp).


Modelling

Buoyancy

The gas vesicles are shaped roughly like a cylinder with a cone at each end, whose cross-section we model as (based mostly on Walsby 1994):

Vesicle Shape.png

We assume the interior of the wall of the gas vesicle is similarly shaped to the exterior, just slightly smaller (the right-most part of the image above illustrates this situation for the left tip of the gas vesicle). This means the different dimensions are related through the equations below. To determine the total volume, just use them with the given width/diameter (at least for the dimensions given in Walsby 1994). To determine the gas volume, use them with wgas and dgas.

w = nm (EM {{todo}} link)
d = nm (EM)
tw = nm (Walsby1994)
a = ° (Walsby1994)
ρgas = kg/m3 (Walsby1994)
ρwall = kg/m3 (Walsby1994)

Vgas = nm3
Mgas = yg
Vwall = nm3
Mwall = yg
Vvesicle = nm3
Mvesicle = yg
ρvesicle = kg/m3
w = total width
tw = thickness of wall (1.8-1.95nm)
d = diameter
a = 77 degrees
ρgas = density of gas in vesicle (kg/m^3 = yg/nm^3)
ρwall = density of vesicle wall (kg/m^3)
wwt = tw/sin(a/2)
wt = (1/2)*d/tan(a/2)
wc = w - 2*wt
Vc = (1/4)*pi*d^2*wc
Vt = (1/12)*pi*d^2*wt
V = Vc+2*Vt
M = ρ*V

wgas = w-2*wwt = width of gas space
dgas = d-2*tw = diameter of gas space
V = Vgas + Vwall

Now we can consider the buoyant density of E. coli with gas vesicles. We have chosen to approach this problem using densities and volume ratios. According to Baldwin1995, Bylund1991 and Poole1977 the density of (wild-type) E. coli is 1100 kg/m3 ±3% under wildly varying conditions. This makes our method easier than trying to directly compute the density of a single cell, due to the fact that the volume can differ wildly (both during the life cycle and from strain to strain) and a lack of concrete data on the number of gas vesicles produced (in E. coli). Note that the computations below assume that the gas vesicles simply add to the existing structures.

ρmedium = kg/m3
ρcell = kg/m3

Vv / Vcv >
Loading graph...
Vc = volume of a cell without gas vesicles
Vv = volume of gas vesicles in cell
Vcv = volume of a cell with gas vesicles (assumed to be Vc+Vv)
ρc = density of a cell without gas vesicles
ρv = density of gas vesicles
ρm = density of medium

The following has to be true if the cell floats:
 Vc*ρc + Vv*ρv < Vcv*ρm
 (Vcv-Vv)*ρc + Vv*ρv < Vcv*ρm
 ρc + (Vv/Vcv)*(ρv-ρc) < ρm
Assume (ρv - ρc)<0
 Vv/Vcv > (ρm - ρc)/(ρv - ρc)
 Vv/Vcv > 1 - (ρm - ρv)/(ρc - ρv)

Explanation of the graph

Three curves are shown, corresponding to how many gas vesicles a cell needs with "our" gas vesicles (unless you changed the constants in the calculator above), the gas vesicles documented in Li 1998
Using a width and diameter of 75nm and 50nm, respectively. Here we assume that their "width" should be interpreted as our diameter, as doing it the other way around would leave no room for a cylinder and they specifically mention that the vesicles appear to be shaped like cylinders with conical ends.
 i 
and the gas vesicles from Anabaena in Walsby 1994
Using a width and diameter of 500nm and 84nm, respectively.
 i 
.

The X-axis depicts the cell density of the part of the cell not occupied by gas vesicles.

The Y-axis depicts the minimum volume fraction of the cell that should consist of gas vesicles to make the cell float.

Missing information

  • Used promotor for expression of the gvp-cluster:
    • Inducible (may be used for proof-of-principle)
    • Constitutive (may be used for proof-of-principle)
    • Metal sensitive
  • What kind of vector was used by Li and Cannon (1995) or Melbourne (2007)? Is there a negative effect of high copy number?
  • What is the maximum amount of pressure gas vesicles can handle? At which depth would this be, how can one put this kind of pressure on a water column?
  • What is the density of gas vesicles in cells (normally or in case of over-expression)
  • Modelling parameters (to be measured):
    • What is the density of the cell without gas vesicles/metal (largely known, but would be good to check), and how is this affected by letting the cell make gas vesicles and/or metal transporters/accumulators and so on?
    • How many gas vesicles are produced? (As volume percentage?)
    • (How fast are they produced?)

-Cyanobacteria Bowen 1965: gas vacuoles made up of gas vesicles (75 nm in diameter and up to 1.0 ,um in length, single wall layer only 2 nm thick) 0,7MPa gives irreversible loss of buoyancy fenotype, but found in next generation.


you can use a nephelometer, to measurement the light scattering of the gas vesicles (Walsby 1994)

Planning and requirements:

  • Modelling:
    • Buoyancy
      • Permeability
      • Number of gasvesicles
      • Where do the gasvesciles end, in hight.
    • Mass of the bacteria (e.coli)
    • How long it takes before it floates
      • How long it take untill it is being expressed
      • How long it will take untill there are enough gasvesicles
      • How does it stay floating
  • Lab:
    • Gvp
      • Cluster of biobricks
      • Vector ordered from article
      • First expression with constutatieve promotor, later with metal sensitive promotor
    • Measurements
      • Where are the bacteria, what are bac concentrations on a certain hight (not necessary???)
        • Making pictures on certain hight and compare with picture of known concentration
      • Do we have gas vesicles?