Team:Cambridge/Bioluminescence/Vibrio Characterisation

From 2010.igem.org

(Difference between revisions)
(New page: {{:Team:Cambridge/Templates/headerMinimalprototype}} {{:Team:Cambridge/Templates/headerbar|colour=#96d446|linkcolour=#6bbe00|title=Project Firefly: Characterisation}} This page describes ...)
 
(12 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:Cambridge/Templates/headerMinimalprototype}}
{{:Team:Cambridge/Templates/headerMinimalprototype}}
-
{{:Team:Cambridge/Templates/headerbar|colour=#96d446|linkcolour=#6bbe00|title=Project Firefly: Characterisation}}
+
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Project Vibrio: Characterisation}}
-
This page describes characterisation for part [http://partsregistry.org/Part:BBa_K325219 BBa_K325219], Red luciferase and LRE operon from L. cruciata under pBAD.
+
This page describes characterisation for part [http://partsregistry.org/Part:BBa_K325909 BBa K325909], the [http://2010.igem.org/Team:Cambridge/Bioluminescence/Bacterial_Luciferases ''lux operon'' from ''Vibrio fischeri''].  
 +
 
 +
*[[Team:Cambridge/Bioluminescence/Vibrio_Characterisation#Description|Description]]
 +
*[[Team:Cambridge/Bioluminescence/Vibrio_Characterisation#Arabinose_to_light|Arabinose to light]]
 +
*[[Team:Cambridge/Bioluminescence/Vibrio_Characterisation#H-NS_mutants|H-NS mutants]]
-
*[[Team:Cambridge/Bioluminescence/Firefly_Characterisation#Description|Description]]
 
-
*[[Team:Cambridge/Bioluminescence/Firefly_Characterisation#Arabinose_to_light|Arabinose to light]]
 
-
*[[Team:Cambridge/Bioluminescence/Firefly_Characterisation#Luciferin_to_light|Luciferin to light]]
 
-
*[[Team:Cambridge/Bioluminescence/Firefly_Characterisation#Effect_of_pH|Effect of pH]]
 
=Description=
=Description=
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-low.jpg|caption=E.Coli (Invitrogen TOP 10) cells transformed with [http://partsregistry.org/Part:BBa_K325909 BBa K325909] (blue light bulb) and [http://partsregistry.org/Part:BBa_K325219 BBa 325219] (red light bulb)}}
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-low.jpg|caption=E.Coli (Invitrogen TOP 10) cells transformed with [http://partsregistry.org/Part:BBa_K325909 BBa K325909] (blue light bulb) and [http://partsregistry.org/Part:BBa_K325219 BBa 325219] (red light bulb)}}
-
This part generates a red-mutant of the luciferase from the Japanese firefly (L.cruciata) as well as the luciferin regenerating enzyme (LRE). It is under the control of an Arabinose induced promoter. D-Luciferin has to be added to obtain light output.
+
This page described the lux operon from Vibrio fischeri. To relieve LuxR control we placed Lux C, D, A, B, E under the pBad promoter.
-
=Arabinose to light=
 
-
This page describes the relationship between Arabinose concentration in the medium with light output. We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocol and plate reader settings used are given below.
 
-
{{:Team:Cambridge/Templates/Nolineheader|header=Data}}
 
-
'''Transfer function of <partinfo>K325219</partinfo>.'''
+
[[Image:250px-Cambridge-iGEMpixels.jpg|thumb|569px|center|'''Figure 1 - E.coli cells (Invitrogen TOP 10) transformed with [http://partsregistry.org/Part:BBa_K325909 BBa K325909] in a 96 well plate. ''']]
-
+
-
[http://partsregistry.org/wiki/images/2/26/IntegratedactiPP%2BLRE.png http://partsregistry.org/wiki/images/thumb/c/c3/Luciferineffect.png/569px-Luciferineffect.png]
+
-
The data points represent the mean of 11 values obtained for light output at 30 min interval from 450 min to 750 min after injection of D-Luciferin. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 33 data points centred around the mean value.
+
=Arabinose to light=
-
 
+
This page describes the relationship between Arabinose concentration in the medium with light output. We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocol and plate reader settings used are given below.  
-
'''Maximum luminescence output of  <partinfo>K325219</partinfo> as a function of Arabinose concentration.'''
+
-
 
+
-
[http://partsregistry.org/wiki/images/0/05/MaximumlumPP%2BLRE.png http://partsregistry.org/wiki/images/thumb/0/05/MaximumlumPP%2BLRE.png/569px-MaximumlumPP%2BLRE.png]
+
-
 
+
-
 
+
-
These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 3 data points centred around the mean value.
+
-
 
+
-
'''Evolution of luminescence with time at different Arabinose concentrations.'''
+
-
 
+
-
[http://partsregistry.org/wiki/images/4/4c/TimePP%2BLRE.png http://partsregistry.org/wiki/images/thumb/4/4c/TimePP%2BLRE.png/569px-TimePP%2BLRE.png]
+
-
 
+
-
The interval between measurements is 30 min. Mean values and error bars are based on 3 time repeats.
+
-
<center>
+
-
{|{{Table}}
+
-
!Data
+
-
!Notes
+
-
!Date Uploaded
+
-
|-
+
-
|[http://partsregistry.org/wiki/images/8/82/BBa_K325219ArabinosetoLight.xls Media:BBa_K325219ArabinosetoLight.xls]
+
-
|Raw data from experiment
+
-
|21/10/2010
+
-
|}
+
-
</center>
+
-
 
+
-
 
+
-
{{:Team:Cambridge/Templates/Nolineheader|header=Protocol}}
+
-
 
+
-
=Luciferin to light=
+
-
 
+
-
The light output is also a function of the concentration of D-Luciferin the media. This page describes the relationship between D-Luciferin concentration and light output. We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocols and plate reader settings used are given below.  
+
{{:Team:Cambridge/Templates/Nolineheader|header=Data}}
{{:Team:Cambridge/Templates/Nolineheader|header=Data}}
-
'''Effect of D-Luciferin concentration on light output from <partinfo>K325219</partinfo>.'''
+
[[Image:BBa_K325909Aracurve.png|thumb|569px|center|'''Figure 1 - Light output of <partinfo>K325909</partinfo> as a function of Arabinose concentration in the media. The values correspond to the peak intensity within 5 hours of adding Arabinose to the media. Data points and error bars correspond to the mean and the standard deviation of 3 time repeats. ''']]
-
 
+
[[Image:BBa_K325909timecourse.png|thumb|569px|center|'''Figure 2 - Evolution of luminescence with time at different Arabinose concentrations for <partinfo>K325909</partinfo>. Measurements were taken every 30 minutes. Data points and error bars correspond to the mean and standard deviation of 3 time repeats. ''']]
-
[http://partsregistry.org/wiki/images/c/c3/Luciferineffect.png http://partsregistry.org/wiki/images/thumb/c/c3/Luciferineffect.png/569px-Luciferineffect.png]
+
-
 
+
-
The data points represent the mean of 31 values obtained for light output at 30 min interval from 1500 min to 2400 min after injection of D-Luciferin. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 31 data points centred around the mean value.
+
-
 
+
-
'''Evolution of luminescence with time at different Arabinose concentrations.'''
+
-
 
+
-
[http://partsregistry.org/wiki/images/b/b9/Luctimecourse.png http://partsregistry.org/wiki/images/thumb/b/b9/Luctimecourse.png/569px-Luctimecourse.png]
+
-
 
+
-
The interval between measurements is 30 min. Mean values and error bars are based on 3 time repeats.
+
<center>
<center>
{|{{Table}}
{|{{Table}}
Line 75: Line 31:
!Date Uploaded
!Date Uploaded
|-
|-
-
|[http://partsregistry.org/wiki/images/9/9a/BBa_K325219luciferintolight.xls Media:BBa_K325219luciferintolight.xls‎]
+
|[[Media:BBa_K325909ArabinosetoLight.xls]]
|Raw data from experiment
|Raw data from experiment
|21/10/2010
|21/10/2010
Line 81: Line 37:
</center>
</center>
-
{{:Team:Cambridge/Templates/Nolineheader|header=Protocol}}
+
=H-NS mutants=
-
#Three 5 ml cultures of [http://openwetware.org/wiki/Endy:M9_media/supplemented supplemented M9 medium] and antibiotic (kanamycin, 20 µg/ml) were inoculated with single colonies (~2mm ø) from a freshly streaked plate of [http://partsregistry.org/Part:BBa_V1000 MG1655] containing <partinfo>BBa_T9002</partinfo>.  One 5 ml culture was inoculated with a single colony from a freshly streaked plate of [http://partsregistry.org/Part:BBa_V1000 MG1655] containing a <partinfo>BBa_T9002</partinfo> mutant (T9002m) lacking a GFP expression device described in the [http://partsregistry.org/Part:BBa_F2620:Stability stability section].
+
It has been shown that the expression of the Vibrio fischeri lux operon when cloned into E. coli was repressed. This repression was linked to the nucleoid protein H-NS. To investigate this effect we cloned the operon into mutant E.coli cells in which the expression of the H-NS protein had been modified.  We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocols and plate reader settings used are given below.  
-
#Cultures were grown in 17 mm test tubes for 15 hrs at 37°C with shaking at 70 rpm.
+
-
#Cultures were diluted 1:1000 into 5.5 ml of fresh medium and grown to an OD600 of 0.15 under the same conditions as before.  This growth took on average 4.5 hrs.
+
-
#Twenty-four 200 µl aliquots of each of the cultures were transferred into a flat-bottomed 96 well plate (Cellstar Uclear bottom, cat. # T-3026-16, Greiner).
+
-
#2 µl of the stock concentrations of the cognate AHL, 3-oxohexanoyl-homoserine lactone ([http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL]]), was added to each well to yield 8 different final concentrations (0, 1E-10, 1E-9, 1E-8, 1E-7, 1E-6, 1E-5 and 1E-4 M). Three replicate wells were measured for each concentration of [http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL].  Three wells were each filled with 200 µl of medium to measure the absorbance background.  Three further wells were each filled with 200 µl of the <partinfo>BBa_T9002</partinfo> mutant culture to measure fluorescent background.
+
-
#The plate was incubated in a [http://openwetware.org/wiki/Endy:Victor3_plate_reader Wallac Victor3 multi-well fluorimeter] (Perkin Elmer) at 37°C and assayed with an automatically repeating protocol of absorbance measurements (600 nm absorbance filter, 0.1 second counting time through 5 mm of fluid), fluorescence measurements (488 nm excitation filter, 525 nm emission filter, 0.5 seconds, CW lamp energy 12901 units), and shaking (1 mm, linear, normal speed, 5 seconds).  Time between repeated measurements was 2 min and 21 s.  Approximately 6 min elapsed between beginning addition of [http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL] to the wells and the first plate reader measurement.  [http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL] was added in order of increasing concentration to minimize GFP synthesis during plate loading.  Cells appear to grow exponentially for the duration of the plate reader measurement protocol (see Figure 2 for representative growth curves).
+
-
#We repeated steps 1 through 6 on three separate days to obtain data for nine colonies from a single plate. 
+
-
#We processed the data to compute the PoPS output from <partinfo>BBa_F2620</partinfo> as described on the [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis Data analysis page].  The data for each colony tested was averaged across the three replicate wells.  The mean for each colony was then averaged to obtain a population mean. The time and dose dependent input-output surface is shown above in Figure 3. Following an initial transient response, device output reached an approximate steady state.
+
-
#The snapshot transfer function in Figure 1 is the 60 min time-slice from the surface shown in Figure 3 (highlighted as a heavy black line).  Error bars in Figure 1 representing the 95% confidence interval in the population for the nine independent samples.  The cyan shaded region represents the range of the nine independent samples.
+
-
#To estimate parameters that characterize the measured transfer function, we used least squares estimation to fit a simple model to the data. A Hill equation derived from simple biochemical equations describes the data well (R<sup>2</sup>=0.99).  In the equation (shown below), P<sub>out</sub> is the PoPS per cell output of <partinfo>BBa_F2620</partinfo>, P<sub>max</sub> is the maximum output level, K is the switch point, and n is the hill coefficient describing the steepness of the transition from low output to high output.
+
-
#To gain further information about the transition region of the transfer function, measurements were subsequently taken at two intermediate [http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL] concentrations (3.3E-09 M and 3.3E-08 M) using the same protocol defined aboveMeasurements were simultaneously taken at a subset of the original concentrations to ensure the new data was consistent with the earlier data.  The new data was processed simultaneously with the original data, with the exception that only six independent colonies were measured for the intermediate [http://partsregistry.org/3OC6HSL 3OC<sub>6</sub>HSL] concentrations.
+
-
 
+
-
=Effect of pH=
+
-
 
+
-
Both the intensity and the spectrum emitted by the luciferase-luciferin reaction has been shown to be higly dependent on the pH of the medium. The main characterisation experiments have been performed in LB Broth at pH 7, so in order to assess this effect cultures with LB and a citrate buffer were prepared (pH = 5.3, pH 6.1 and pH = 7) This page describes the results of these experiments. We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocols and plate reader settings used are given below.  
+
{{:Team:Cambridge/Templates/Nolineheader|header=Data}}
{{:Team:Cambridge/Templates/Nolineheader|header=Data}}
-
'''Maximum light output within 5 hours of D-luciferin injection at different pH values.'''
+
[[Image:BBa_K325909AraK28.png|thumb|569px|center|'''Figure 1 - Peak light output from <partinfo>K325909</partinfo> cloned into H-NS mutant JM 230 H-NS -205::tn10. The data points and the error bar are the mean and standard deviation obtained by 3 tim repeats. ''']]
-
 
+
[[Image:BBa_K325909timecourseK28.png|thumb|569px|center|'''Figure 2 - Evolution of light output from <partinfo>K325909</partinfo> cloned into H-NS mutant JM 230 H-NS -205::tn10 with time at different Arabinose concentrations. The data points and the error bar are the mean and standard deviation obtained by 3 time repeats. Measurements were taken every 30 minutes.  ''']]
-
[http://partsregistry.org/wiki/images/e/e8/Phhistogram.png http://partsregistry.org/wiki/images/thumb/e/e8/Phhistogram.png/569px-Phhistogram.png]
+
[[Image:BBa_K325909AraR28.png|thumb|569px|center|'''Figure 3 - Figure 3 - Peak light output from <partinfo>K325909</partinfo> cloned into H-NS mutant [http://www.ecoliwiki.net/colipedia/index.php/BW25113 BW25113 DELTA H-NS::kan]. The data points and the error bar are the mean and standard deviation obtained by 3 tim repeats.''']]
-
 
+
[[Image:BBa_K325909timecourseR28.png|thumb|569px|center|'''Figure 4 - Evolution of light output from <partinfo>K325909</partinfo> cloned into H-NS mutant [http://www.ecoliwiki.net/colipedia/index.php/BW25113 BW25113 DELTA H-NS::kan] with time at different Arabinose concentrations. The data points and the error bar are the mean and standard deviation obtained by 3 time repeats. Measurements were taken every 30 minutes.''']]
-
These values are the mean of 3 readings. The corresponding error bars represent an interval of twice the standard deviation across the 3 data points centred around the mean value.
+
-
 
+
-
'''Evolution of light output at different values of pH.'''
+
-
 
+
-
[http://partsregistry.org/wiki/images/d/d8/Phtimecourse.png http://partsregistry.org/wiki/images/thumb/d/d8/Phtimecourse.png/569px-Phtimecourse.png]
+
-
 
+
-
Measurements are taken every 20 min. These values are the mean of 3 readings. The corresponding error bars represent an interval of twice the standard deviation across the 3 data points centred around the mean value.
+
<center>
<center>
{|{{Table}}
{|{{Table}}
Line 118: Line 53:
!Date Uploaded
!Date Uploaded
|-
|-
-
|[http://partsregistry.org/wiki/images/6/64/BBa_K325219pheffect.xls Media:BBa_K325219pheffect.xls]
+
|[[Media:BBa_K325909Mutants.xls]]
|Raw data from experiment
|Raw data from experiment
|21/10/2010
|21/10/2010
Line 124: Line 59:
</center>
</center>
-
{{:Team:Cambridge/Templates/Nolineheader|header=Protocol}}
 
-
#The protocol can be found as [http://2010.igem.org/Team:Cambridge/Notebook/Week11 Experiment 110].
 
=Compatibility=
=Compatibility=
-
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=cell ''Chassis:''] Device has been shown to work in ''Top 10 (Invitrogen)''
+
[http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=cell ''Chassis:''] Device has been shown to work in ''Top 10 (Invitrogen)'', [http://www.ecoliwiki.net/colipedia/index.php/BW25113 BW25113 DELTA H-NS::kan] and H-NS mutant JM 230 H-NS -205::tn10.<br>
[[Plasmid backbones|''Plasmids:'']] Device has been shown to work on ''<partinfo>pSB1C3</partinfo>'' <br>
[[Plasmid backbones|''Plasmids:'']] Device has been shown to work on ''<partinfo>pSB1C3</partinfo>'' <br>
=References=
=References=
-
[http://www.ncbi.nlm.nih.gov/pubmed/18949818 '''[1&#x5d;:'''] S.M. Marques and J.C.G. Esteves da Silva, (2009) Firefly Bioluminescence: A Mechanistic Approach of Luciferase Catalyzed Reactions,''Life'' '''61''', 6-17.
 
 +
[http://www.jstor.org/stable/4449975 '''[1&#x5d;:'''] J. Slock, (1995) Transformation Experiments Using Bioluminescence Genes of ''Vibrio fischeri'',''The American Biology Teacher'', '''57''', 225-227.
-
[http://www.nature.com/nature/journal/v440/n7082/abs/nature04542.html '''[2&#x5d;:'''] T. Nakatsu ''et al.'' (2006) Structural Basis for the spectral difference in luciferase bioluminescence, ''Nature'' '''440'''(16), 372-376.
+
[http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055 '''[2&#x5d;:'''] E.A. Meighen (1988) Enzymes and genes from the ''lux'' operons of bioluminescent bacteria, ''Annual Reviews in Microbiology'' '''42''', 151-176.
 +
[http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.28.120194.001001 '''[3&#x5d;:'''] E.A. Meighen, (1994) Genetics of bacterial bioluminescence, ''Annual Reviews of Genetics'', '''28''', 117-139.
-
[http://www.ncbi.nlm.nih.gov/pubmed/11457857 '''[3&#x5d;:'''] K. Gomi and N. Kajiyama, (2001) Oxyluciferin, a Luminescence Product of Firefly Luciferase, Is Enzymatically Regenerated into Luciferin, ''The Journal of Biological Chemistry'', '''276'''(39), 36508-36513.
+
[http://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291099-1271%28199807/08%2913:4%3C185::AID-BIO486%3E3.0.CO;2-U/abstract '''[4&#x5d;:'''] S. Ulitzur, (1998) H-NS controls the transcription of three promoters of ''Vibrio fischeri lux'' cloned in ''Escherichia coli'',''Journal of Bioluminescence and Chemiluminescence'', '''13'''(4), 185-188.
 +
[http://www.nature.com/nature/journal/v444/n7117/full/nature05283.html '''[5&#x5d;:'''] R.T. Dame ''et al.'', (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation,''Nature'', '''444''', 387-390.
{{:Team:Cambridge/Templates/footer}}
{{:Team:Cambridge/Templates/footer}}

Latest revision as of 23:24, 27 October 2010