Team:WashU StLouis/Project/nif

From 2014.igem.org

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<h3> Nif Cluster in E. Coli </h3>
+
-
<p> Insert Nif Project here</p>
+
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<h3> Data </h3>
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-
<p> add some table here </p>
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<h3> Results </h3>
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<p> add some table here </p>
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<h3> References </h3>
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<p> Don't forget to site </p>
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 +
<body>
 +
<div style="text-align: center;">
 +
<h1>Introduction</h1>
 +
</div>
 +
Nitrogen is abundant in the earth’s atmosphere but, unlike carbon,
 +
cannot be directly assimilated by plants.[1] Nitrogen can be directly
 +
fixed from the atmosphere by some Cyanobacteria such as <span
 +
style="font-style: italic;">Cyanothece</span> 51142, which possesses
 +
the enzyme nitrogenase translated from <span
 +
style="font-style: italic;">nif</span> genes. Some plant species have
 +
evolved close symbiotic associations with nitrogen-fixing bacteria.
 +
Engineering crops with the capability to fix their own nitrogen could
 +
one day address the problems created by the abuse of fertilizers in
 +
agriculture. This could be achieved either by expression of a
 +
functional nitrogenase enzyme in the cells of the crop or through
 +
transferring the capability to form a symbiotic association with
 +
nitrogen-fixing bacteria. Our project mainly focuses on expressing the <span
 +
style="font-style: italic;">nif</span> clusters in <span
 +
style="font-style: italic;">E. coli </span>strains under various
 +
conditions in order to study the <span style="font-style: italic;">nif</span>
 +
system in simpler internal environment of prokaryotic cells.<br>
 +
<br>
 +
<div style="text-align: center;">
 +
<h1>Objectives</h1>
 +
</div>
 +
Rapidly growing, with high survival rate in environment, <span
 +
style="font-style: italic;">E. coli </span>has many attributes that
 +
make it an ideal candidate for use as a model organism, which is a
 +
species that is extensively studied to understand a specific
 +
phenomenon—we expect that the knowledge gained can be applied to other
 +
species as well in future.<br>
 +
The genomes of many strains of <span style="font-style: italic;">E.
 +
coli</span> have been sequenced. These sequences have been scrutinized
 +
so heavily that the way the cell works is very well understood, and
 +
changing and manipulating the DNA sequence will lead to predictable
 +
results.&nbsp; Thus, from the previous research of internal energy
 +
management and nutritional capability on various strains of E. coli, we
 +
have proposed to selected four strains[2], JM109, BL21(DE3), WM1788,
 +
and DH5α to carry plasmid pNif51142, which insert the <span
 +
style="font-style: italic;">nif </span>cluster from <span
 +
style="font-style: italic;">Cyanothece</span> sp. 51142, therefore
 +
expressing the nitrogenase activity. The general objective is to adjust
 +
parameters of environmental conditions to show nitrogen-fixing activity
 +
in <span style="font-style: italic;">E. coli</span> strains and
 +
eventually adapt to the light-controlling promoter system from the side
 +
of our team. <br>
 +
<br>
 +
<div style="text-align: center;">
 +
<h1>Overview</h1>
 +
</div>
 +
Our project consisted of three different phases. <br>
 +
Phase 1: Electro-Transformation of plasmid pNif51142 into <span
 +
style="font-style: italic;">E. coli</span> strains<br>
 +
Phase 2: Determine the optimal conditions for cell survival with
 +
plasmid pNif51142 in <span style="font-style: italic;">E. coli</span><br>
 +
Phase 3: Measure nitrogen fixation activity under determined optimal
 +
conditions in <span style="font-style: italic;">E. coli</span> strains<br>
 +
<br>
 +
<br>
 +
<div style="text-align: center; font-weight: bold;">Phase 1:
 +
Electro-Transformation of plasmid pNif51142 into <span
 +
style="font-style: italic;">E. coli </span>strains<br>
 +
</div>
 +
<br>
 +
<table
 +
style="text-align: left; width: 1348px; margin-left: auto; margin-right: auto; height: 551px;"
 +
border="0" cellpadding="5" cellspacing="5">
 +
<tbody>
 +
<tr>
 +
<td style="vertical-align: top; text-align: center;"><img
 +
src="https://static.igem.org/mediawiki/2014/4/4b/WashU_nifcluster_size.png"
 +
alt="nif cluster" style="width: 700px; height: 504px;"><br>
 +
Figure above: <span style="font-style: italic;">nif</span> cluster of <span
 +
style="font-style: italic;">Cyanothece </span>sp. 51142 containing
 +
all the necessary genes for nitrogen fixation<br>
 +
</td>
 +
<td style="vertical-align: middle; text-align: justify;">Due to
 +
the large size of the plasmid pNif51142, 37,630bp, it was very
 +
challenging to transform it into E. coli strains. <br>
 +
&nbsp;<br>
 +
To successfully transform pNif51142, we used Electro-Transformation,
 +
also known as Electroporation.&nbsp; Electroporation provides a method
 +
of
 +
transforming E. coli to efficiencies greater than are possible with the
 +
best chemical methods. By subjecting mixtures of cells and DNA to
 +
exponentially decaying fields of very high initial amplitude, we were
 +
able to deliver the plasmid into all of E. coli strains that were
 +
tested in the project.<br>
 +
<br>
 +
<span style="font-weight: bold;">Results:</span><br>
 +
According to the gel running and antibiotic testing, bands in the gel
 +
and the survival of all strains transformed in antibiotic Kanamycin
 +
(there was an cluster of Kanamycin-resistant marker gene in sequence of
 +
pNif51142) both prove that the Electro-Transformation was successful.<br>
 +
</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<br>
 +
<div style="text-align: center;"><span style="font-weight: bold;">Phase
 +
2: Determine the optimal conditions for cell survival with plasmid
 +
pNif51142 in </span><span
 +
style="font-style: italic; font-weight: bold;">E. coli</span><br
 +
style="font-style: italic;">
 +
</div>
 +
<span style="font-weight: bold;">Testing Media:</span> Minimal M9<br>
 +
<br>
 +
<span style="font-weight: bold;">Conditions/Parameters Tested: </span><br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;<span style="font-weight: bold;">
 +
Carbon Source:</span> Glucose (1mM, 10mM, 100mM)<br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">Nitrogen
 +
Source:</span> Glutamine (1mM, 10mM, 100mM), Glutamate (1mM, 10mM,
 +
100mM), NH4Cl (1mM, 10mM,100mM) All Concentration range determined by
 +
[3]<br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">Temperature:</span>
 +
30°C, 37°C, 40°C<br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">pH:</span>
 +
6, 7, 8<br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">O2
 +
Level: </span>Anaerobic or Aerobic <br>
 +
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">Strains
 +
of <span style="font-style: italic;">E. coli</span></span>: JM109,
 +
BL21(DE3), WM1788, DH5α&nbsp;&nbsp;&nbsp; <br>
 +
<br>
 +
<table
 +
style="text-align: left; width: 556px; height: 349px; margin-left: auto; margin-right: auto;"
 +
border="1" cellpadding="5" cellspacing="0">
 +
<tbody>
 +
<tr>
 +
<td style="text-align: center;">Target<br>
 +
Strain <br>
 +
</td>
 +
<td style="text-align: center;">JM109&nbsp; <br>
 +
</td>
 +
<td style="text-align: center;">BL21(DE3) <br>
 +
</td>
 +
<td style="text-align: center;">WM1788</td>
 +
<td style="text-align: center;">DH5α</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">Experimental Plates <br>
 +
</td>
 +
<td style="text-align: center;">JM 109 strain w/ plasmid<br>
 +
<br>
 +
Antibiotic <br>
 +
</td>
 +
<td style="text-align: center;">BL21(DE3) strain w/ plasmid<br>
 +
<br>
 +
Antibiotic</td>
 +
<td style="text-align: center;">WM1788 strain w/ plasmid<br>
 +
<br>
 +
Antibiotic <br>
 +
</td>
 +
<td style="text-align: center;">DH5α strain w/ plasmid<br>
 +
<br>
 +
Antibiotic</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">Positive Control</td>
 +
<td style="text-align: center;">JM 109 strain w/o plasmid<br>
 +
<br>
 +
No antibiotic</td>
 +
<td style="text-align: center;">BL21(DE3) strain w/o plasmid<br>
 +
<br>
 +
No antibiotic</td>
 +
<td style="text-align: center;"> WM1788 strain w/o plasmid<br>
 +
<br>
 +
No antibiotic</td>
 +
<td style="text-align: center;">DH5α strain w/o plasmid<br>
 +
<br>
 +
No antibiotic</td>
 +
</tr>
 +
<tr>
 +
<td style="text-align: center;">Negative Control <br>
 +
</td>
 +
<td style="text-align: center;"> JM 109 strain w/o plasmid<br>
 +
<br>
 +
Antibiotic</td>
 +
<td style="text-align: center;">BL21(DE3) strain w/o plasmid <br>
 +
<br>
 +
Antibiotic</td>
 +
<td style="text-align: center;">WM1788 strain w/o plasmid<br>
 +
<br>
 +
Antibiotic</td>
 +
<td style="text-align: center;">DH5α strain w/out plasmid<br>
 +
<br>
 +
Antibiotic</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<br>
 +
<table
 +
style="text-align: left; width: 1348px; height: 418px; margin-left: auto; margin-right: auto;"
 +
border="0" cellpadding="5" cellspacing="5">
 +
<tbody>
 +
<tr>
 +
<td style="vertical-align: top; text-align: justify;"><img
 +
style="width: 628px; height: 389px;" alt="nif genes"
 +
src="https://static.igem.org/mediawiki/2014/e/e4/WashU_nifgenes.png"><br>
 +
<br>
 +
</td>
 +
<td style="vertical-align: top; text-align: justify;">Due to the
 +
oxidative properties of oxygen, most nitrogenases are
 +
irreversibly inhibited by dioxygen, which degradatively oxidizes the
 +
Fe-S cofactors. This requires mechanisms for nitrogen fixers to protect
 +
nitrogenase from oxygen in vivo. Hence in our experiment, we firstly
 +
selected anaerobic condition as part of preparation step for the
 +
nitrogenase activity testing.<br>
 +
<br>
 +
<br>
 +
<span style="font-weight: bold;">Results:</span><br>
 +
In the minimal M9 media, all possible combinations of parameters listed
 +
above were tested. <br>
 +
None of the concentrations of glucose had any affect on the growth of <span
 +
style="font-style: italic;">E.
 +
coli</span>. It was expected that as the concentration of glucose
 +
increased,
 +
the growth of <span style="font-style: italic;">E. coli</span> also
 +
increased. However, the variation between
 +
the concentrations of glucose may have been too small for a noticeable
 +
increase in <span style="font-style: italic;">E. coli</span> growth as
 +
the concentration of glucose increased.
 +
Also, even the maximum concentration of glucose tested, 100mM, may have
 +
been too low to affect the growth of <span style="font-style: italic;">E.
 +
coli</span> to an observable extent.
 +
Eventually, 10mM was determined to be the optimal glucose concentration
 +
for the purpose of least interference possible in solution. <br>
 +
NH4Cl as minimal nitrogen source was proven to be not suitable for <span
 +
style="font-style: italic;">E. coli</span>
 +
growth at any concentration as the OD600 testing results showed that
 +
cell density didn’t change throughout the time. It was probably due to
 +
the permeability of cell membrane was limited for NH4+ and Cl- ions.
 +
Eventually Glutamate at concentration of 10mM supported cell growth the
 +
best and thus chosen as part of optimal environment condition.<br>
 +
<br>
 +
With CASAmino solution’s buffering utility, the pH was controlled
 +
little bit below 7 but close to 7. <br>
 +
<br>
 +
To protect the iron core of the nitrogenase, temperature of 30°C and
 +
Anaerobic were both determined not for cell growth but for nitrogenase
 +
activity testing, which is the next phase.<br>
 +
</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<br>
 +
<div style="text-align: center; font-weight: bold;">Phase 3: Measure
 +
nitrogen fixation activity under determined optimal conditions in E.
 +
coli strains<br>
 +
</div>
 +
<br>
 +
<table
 +
style="text-align: left; width: 100%; height: 271px; margin-left: auto; margin-right: auto;"
 +
border="0" cellpadding="5" cellspacing="5">
 +
<tbody>
 +
<tr>
 +
<td style="vertical-align: top; text-align: justify;">We
 +
used&nbsp; an Acetylene Reduction Assay to examine the nitrogenase
 +
activity
 +
for JM109, BL21(DE3), Top10, DH5α at different cell density referred by
 +
OD600 values.<br>
 +
<br>
 +
<br>
 +
<span style="font-weight: bold;">Results:</span><br>
 +
1) Of the four <span style="font-style: italic;">E. coli</span>
 +
strains tested, JM109 and WM1788 showed strongest nitrogenase activity.<br>
 +
&nbsp;<br>
 +
2) The linear relationship between nitrogen fixation activity and time
 +
matches that seen in nature. <br>
 +
<br>
 +
3) Optimal conditions determined: <br>
 +
<ul>
 +
<li>glucose as carbon-source</li>
 +
<li>glutamate as
 +
nitrogen-source</li>
 +
<li>LB as inoculating media</li>
 +
<li>minimal M9 as testing media
 +
for GC assay</li>
 +
<li>anaerobic environment</li>
 +
<li>30 °C during the overnight
 +
preparation</li>
 +
</ul>
 +
</td>
 +
<td style="vertical-align: top;"><img
 +
style="width: 800px; height: 476px;"
 +
alt="Acetylene reduction assay results"
 +
src="https://static.igem.org/mediawiki/2014/f/ff/WashU_ARA_results.png"><br>
 +
</td>
 +
</tr>
 +
</tbody>
 +
</table>
 +
<div style="text-align: center;">
 +
<h1>Citation</h1>
 +
</div>
 +
1: Christian Rogers, Giles E. D. Oldroyd. Journal of Experimental
 +
Botany Advance Access., 2014 May; 65(8):1939-46<br>
 +
2: Heladia Salgado, Socorro Gama, César Bonavides‐Martínez and Julio
 +
Collado‐Vides. Oxford Journals of Nucleic Acid Research., 2003 October;
 +
32(1):303-306<br>
 +
3: Liying Wang, Ray Dixon. PLOS Genetics., 2013 Oct 17; 9(10): 3865–3876<br>
 +
4: Temme, Zhao, Voigt. PNAS., 2012 March 23; 109(18): 7085–7090<br>
 +
<br>
 +
<br>
 +
</body>
</td>
</td>
</tr>
</tr>

Revision as of 22:49, 15 October 2014



Introduction

Nitrogen is abundant in the earth’s atmosphere but, unlike carbon, cannot be directly assimilated by plants.[1] Nitrogen can be directly fixed from the atmosphere by some Cyanobacteria such as Cyanothece 51142, which possesses the enzyme nitrogenase translated from nif genes. Some plant species have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering crops with the capability to fix their own nitrogen could one day address the problems created by the abuse of fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. Our project mainly focuses on expressing the nif clusters in E. coli strains under various conditions in order to study the nif system in simpler internal environment of prokaryotic cells.

Objectives

Rapidly growing, with high survival rate in environment, E. coli has many attributes that make it an ideal candidate for use as a model organism, which is a species that is extensively studied to understand a specific phenomenon—we expect that the knowledge gained can be applied to other species as well in future.
The genomes of many strains of E. coli have been sequenced. These sequences have been scrutinized so heavily that the way the cell works is very well understood, and changing and manipulating the DNA sequence will lead to predictable results.  Thus, from the previous research of internal energy management and nutritional capability on various strains of E. coli, we have proposed to selected four strains[2], JM109, BL21(DE3), WM1788, and DH5α to carry plasmid pNif51142, which insert the nif cluster from Cyanothece sp. 51142, therefore expressing the nitrogenase activity. The general objective is to adjust parameters of environmental conditions to show nitrogen-fixing activity in E. coli strains and eventually adapt to the light-controlling promoter system from the side of our team.

Overview

Our project consisted of three different phases.
Phase 1: Electro-Transformation of plasmid pNif51142 into E. coli strains
Phase 2: Determine the optimal conditions for cell survival with plasmid pNif51142 in E. coli
Phase 3: Measure nitrogen fixation activity under determined optimal conditions in E. coli strains


Phase 1: Electro-Transformation of plasmid pNif51142 into E. coli strains

nif cluster
Figure above: nif cluster of Cyanothece sp. 51142 containing all the necessary genes for nitrogen fixation
 Due to the large size of the plasmid pNif51142, 37,630bp, it was very challenging to transform it into E. coli strains.
 
To successfully transform pNif51142, we used Electro-Transformation, also known as Electroporation.  Electroporation provides a method of transforming E. coli to efficiencies greater than are possible with the best chemical methods. By subjecting mixtures of cells and DNA to exponentially decaying fields of very high initial amplitude, we were able to deliver the plasmid into all of E. coli strains that were tested in the project.

Results:
According to the gel running and antibiotic testing, bands in the gel and the survival of all strains transformed in antibiotic Kanamycin (there was an cluster of Kanamycin-resistant marker gene in sequence of pNif51142) both prove that the Electro-Transformation was successful.

Phase 2: Determine the optimal conditions for cell survival with plasmid pNif51142 in E. coli
Testing Media: Minimal M9

Conditions/Parameters Tested:
        Carbon Source: Glucose (1mM, 10mM, 100mM)
        Nitrogen Source: Glutamine (1mM, 10mM, 100mM), Glutamate (1mM, 10mM, 100mM), NH4Cl (1mM, 10mM,100mM) All Concentration range determined by [3]
        Temperature: 30°C, 37°C, 40°C
        pH: 6, 7, 8
        O2 Level: Anaerobic or Aerobic
        Strains of E. coli: JM109, BL21(DE3), WM1788, DH5α   

Target
Strain
JM109 
BL21(DE3)
WM1788 DH5α
Experimental Plates
JM 109 strain w/ plasmid

Antibiotic
BL21(DE3) strain w/ plasmid

Antibiotic		 WM1788 strain w/ plasmid

Antibiotic
DH5α strain w/ plasmid

Antibiotic
Positive Control JM 109 strain w/o plasmid

No antibiotic		 BL21(DE3) strain w/o plasmid

No antibiotic		 WM1788 strain w/o plasmid

No antibiotic		 DH5α strain w/o plasmid

No antibiotic
Negative Control
JM 109 strain w/o plasmid

Antibiotic		 BL21(DE3) strain w/o plasmid

Antibiotic		 WM1788 strain w/o plasmid

Antibiotic		 DH5α strain w/out plasmid

Antibiotic

nif genes

 Due to the oxidative properties of oxygen, most nitrogenases are irreversibly inhibited by dioxygen, which degradatively oxidizes the Fe-S cofactors. This requires mechanisms for nitrogen fixers to protect nitrogenase from oxygen in vivo. Hence in our experiment, we firstly selected anaerobic condition as part of preparation step for the nitrogenase activity testing.


Results:
In the minimal M9 media, all possible combinations of parameters listed above were tested.
None of the concentrations of glucose had any affect on the growth of E. coli. It was expected that as the concentration of glucose increased, the growth of E. coli also increased. However, the variation between the concentrations of glucose may have been too small for a noticeable increase in E. coli growth as the concentration of glucose increased. Also, even the maximum concentration of glucose tested, 100mM, may have been too low to affect the growth of E. coli to an observable extent. Eventually, 10mM was determined to be the optimal glucose concentration for the purpose of least interference possible in solution.
NH4Cl as minimal nitrogen source was proven to be not suitable for E. coli growth at any concentration as the OD600 testing results showed that cell density didn’t change throughout the time. It was probably due to the permeability of cell membrane was limited for NH4+ and Cl- ions. Eventually Glutamate at concentration of 10mM supported cell growth the best and thus chosen as part of optimal environment condition.

With CASAmino solution’s buffering utility, the pH was controlled little bit below 7 but close to 7.

To protect the iron core of the nitrogenase, temperature of 30°C and Anaerobic were both determined not for cell growth but for nitrogenase activity testing, which is the next phase.

Phase 3: Measure nitrogen fixation activity under determined optimal conditions in E. coli strains

We used  an Acetylene Reduction Assay to examine the nitrogenase activity for JM109, BL21(DE3), Top10, DH5α at different cell density referred by OD600 values.


Results:
1) Of the four E. coli strains tested, JM109 and WM1788 showed strongest nitrogenase activity.
 
2) The linear relationship between nitrogen fixation activity and time matches that seen in nature.

3) Optimal conditions determined:
  • glucose as carbon-source
  • glutamate as nitrogen-source
  • LB as inoculating media
  • minimal M9 as testing media for GC assay
  • anaerobic environment
  • 30 °C during the overnight preparation
 Acetylene reduction assay results

Citation

1: Christian Rogers, Giles E. D. Oldroyd. Journal of Experimental Botany Advance Access., 2014 May; 65(8):1939-46
2: Heladia Salgado, Socorro Gama, César Bonavides‐Martínez and Julio Collado‐Vides. Oxford Journals of Nucleic Acid Research., 2003 October; 32(1):303-306
3: Liying Wang, Ray Dixon. PLOS Genetics., 2013 Oct 17; 9(10): 3865–3876
4: Temme, Zhao, Voigt. PNAS., 2012 March 23; 109(18): 7085–7090

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