Team:Calgary/Project/OSCAR/Decarboxylation

From 2012.igem.org

(Difference between revisions)
 
(122 intermediate revisions not shown)
Line 1: Line 1:
{{Team:Calgary/TemplateProjectBlue|
{{Team:Calgary/TemplateProjectBlue|
-
TITLE=Decarboxylation|proj_o|
+
TITLE=Decarboxylation|
CONTENT=<html>
CONTENT=<html>
Line 6: Line 6:
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Decarboxylation_Low-Res.png" style="float: right; padding: 10px; width: 300px;"></img>
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Decarboxylation_Low-Res.png" style="float: right; padding: 10px; width: 300px;"></img>
-
<h3>Why Decarboxylation?</h3>
+
<h2>Why Decarboxylation?</h2>
-
<p>Though there is great diversity between the many possible compounds termed “naphthenic acids” found in tailings ponds, all share the common chemical feature of a carboxylic acid group. This particular group is known to be the primary cause for the toxicity of these compounds, allowing them to enter through cell membranes and destroy cells. Naphthenic acids are a very problematic component of the tailings ponds, and are not easily degraded under regular circumstances. They are known to leak into local environments and cause many problems for wildlife.</p>  
+
<p>Among the toxins found in the tailing ponds, naphthenic acids (NAs) are among the most harmful and the most common. Though there is great diversity within the NAs class of compounds, all share the common chemical feature of a carboxylic acid group. The carboxyl group is the primary cause for their toxicity, allowing these chemicals to traverse cell membranes and react with cellular materials (Frank <i>et al</i>. 2009). NAs are recalcitrant (not easily degraded), potentially harmful to the surrounding ecosystem (Clemente & Fedorak, 2005) and corrosive to extraction and transport equipment of petroleum materials (Slavcheva <i>et al</i>. 1999).  Corrosion of pipelines leads to higher maintenance costs as well as the grim possibility of these and other toxins leaking into the environment. 
 +
There is a need for methods to degrade NAs that are not prohibitively expensive or that would result in production of other hazardous chemicals.</p>  
-
<p>Additionally, removing the carboxylic acid group(s) is of great importance in the conversion of these contaminants to biofuel. Since naphthenic acids are a widely varying and unspecific mixture of compounds, an enzymatic process with very low substrate specificity is necessary, as particularly specific enzymes would not be able to universally decarboxylate all naphthenic acid substrates found in tailings ponds. Without a carboxylic acid group, and with the removal of sulphur and nitrogen contaminants, an alkane suitable for use as fuel can be obtained. The goal of this subproject was to find a suitable pathway to accomplish the decarboxylation of naphthenic acids with the broadest specificity possible.</p>
+
<p>The main goal of OSCAR is to turn toxins like these into useable hydrocarbons by removing the carboxylic acid group(s) (Behar & Albrecht, 1984).  
-
<h3>The PetroBrick</h3>
+
Since NAs from petroleum deposits are a variable mixture, an enzymatic process with broad specificity is necessary. With the removal of the carboxylic acid moiety, we aim to produce alkanes suitable for use as fuel. The goal of this subproject was to find one or more suitable pathways to accomplish the decarboxylation of compounds such as NAs with the broadest specificity.</p>
-
<p>As part of their submission for the 2011 iGEM competition, the University of Washington included a part called the PetroBrick, consisting of two genes intended to establish a metabolic pathway to convert fatty acids to alkanes in vivo. The first gene in the pathway encodes acyl-ACP reductase (AAR), reducing fatty acids bound to ACP to fatty aldehydes, while the second encodes aldehyde decarbonylase (ADC) to subsequently cleave the entire aldehyde group, resulting in a hydrocarbon chain.</p>
 
-
<p>Since the end goal of the decarboxylation project was fuel production, and because the University of Washington’s project provided an easily accessible route to a decarboxylation pathway already available in the BioBrick registry, the PetroBrick was selected as a starting point to this issue. The problem with using the PetroBrick to decarboxylate naphthenic acids was immediately apparent: the first enzyme in particular (AAR) was highly specific for fatty acids bound to ACP. While this is not a concern for producing alkanes from fatty acid biosynthesis, it was not considered to be particularly compatible with naphthenic acid degradation. Therefore we sought an alternate reductase to accompany AAR in the pathway, which would be the CAR gene. </p>
+
<h2>The PetroBrick</h2>
-
<p>Meanwhile, testing proceeded with the PetroBrick. Cultures were grown in a production media designed by Washington in 2011 to be conducive towards alkane production and incubated for 48 hours. Afterwards, an extraction with ethyl acetate was performed to separate the alkanes. Not only was production of alkanes from glucose successful, as the University of Washington had earlier demonstrated, but we were able to optimize the PetroBrick to produce alkane and alkene hydrocarbons from naphthenic acids.</p>
+
<p>The 2011 Washington iGEM team developed the PetroBrick (<a
-
<p>Initially the ability for the Petrobrick to produce alkanes from glucose was analyzed in order to verify that the Petrobrick was working as described by the 2011 Washington team. This was demonstrated in Figure 1 and 2. 
+
href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025">BBa_K590025.</a>), a BioBrick consisting of two primary genes. These include acyl-ACP reductase (<i><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032">AAR</a></i>), which reduces fatty acids bound to ACP to fatty aldehydes, and a second gene called aldehyde decarbonylase (<i><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031">ADC</a></i>), which subsequently cleaves the entire aldehyde group and results in a hydrocarbon chain (Sukovich, 2010). Essentially this allows for hydrocarbons to be produced from glucose.  What we realized though, is that the fatty acids that the PetroBrick targets, have a very similar structure to NAs.</p>
 +
</html>[[File:UCalgary-Fatty-Acids-vs-NAs.jpg|550px|centre|thumb|Figure 1: A comparison of the structure of fatty acids and naphthenic acids]]<html>
 +
<p>We predicted that the PetroBrick may have the potential to turn NAs in to hydrocarbons and be a perfect solution to remediating NAs!  First though, we needed to show that the PetroBrick did in fact work as expected.  We had some difficulty with the DNA from the registry and had to request the constructs directly from the Washington team.  Once we had the PetroBrick, we needed to verify that the PetroBrick would work in our hands as it did for the <a href="https://2011.igem.org/Team:Washington">2011 Washington team</a>.
-
</html>[[File:Calgary2012_PetrobrickVerificationGC.jpg|center|500px]]<html>
+
Figures 2 and 3 demonstrate the function of the PetroBrick.</p>
-
<p>Figure 1: Gas Chromatograph demonstrating the differences in peak composition between an E. coli control and the Petrobrick.  There was a large increase in a peak with a retention time of 12.25 min. suggesting that the Petrobrick was producing a new compound.</p>
+
-
</html>[[File:Calgary2012_PetrobrickVerificationMS.jpg|center|500px]]<html>
+
</html>[[File:Calgary2012_PetrobrickVerificationGC.jpg|center|thumb|Figure 2: Gas chromatograph of the differences in peak composition between an <i>E. coli</i> control and the PetroBrick. There was a large increase in a peak with a retention time of 12.25 min, suggesting that the PetroBrick was producing a new hydrocarbon compound.|650px]]<html>
-
<p>Figure 2: Mass Spectra of the gas chromatograph peak at 12.25 min.  The spectra suggests that the Petrobrick is selectively producing a C15 alkane.  This is what was expected as determined by the Washington 2011 iGEM team.</p>
+
-
<p>With the Petrobrick shown to be able to successfully produce alkanes, it was then tested to see if naphthenic acids could be selectively converted into alkanes. This experiment used commercially available naphthenic acid fractions including a large number of different naphthenic acid compounds.
+
</html>[[File:Calgary2012_PetrobrickVerificationMS.jpg|center|thumb|Figure 3: Mass spectrum of the gas chromatograph peak at 12.25 min. This spectra suggests that the PetroBrick is selectively producing a C15 alkane, which resembles the results from the Washington 2011 iGEM team.|750px]]<html>
-
<h3> Results of the PetroBrick</h3>
+
<p>With the PetroBrick able to successfully produce alkanes, we next wanted to test the PetroBrick on NAs to see if they could be selectively converted into alkanes!  This experiment used commercial NA fractions, which included a large number of different complex NA compounds.  </p>
 +
<a name="Petrobrick"></a><h2>Successful conversion of NAs into hydrocarbons!</h2>
-
</html>[[File:Ucalgary_Decarboxylation_NaphthenicAcids_Results.png|center|700px]]<html>
+
</html>[[File:Ucalgary_Decarboxylation_NaphthenicAcids_Results.png|center|thumb|Figure 4: The relative intensity of alkane production from NAs as measured with a GC-MS in <i>E. coli</i> with and without the PetroBrick. A concentrated NA standard was included for comparison of peaks.|700px]]<html>
-
<p>Figure 1: The relative intensity of alkane production over a retention time in both E.coli that contain the PetroBrick, and in E.coli that are lacking the PetroBrick, as measured with GC-MS. Naphthenic acids were used as a substrate. A naphthenic acid standard was required to compare peaks.</p>
+
</html>[[File:Ucalgary_Decarboxylation_Alkanes_Alkenes_Results.png|center|700px|thumb|Figure 5: Mass spectra of alkanes and alkenes produced from NAs with <i>E. coli</i> containing the PetroBrick as in Figure 2. Relative intensity of mass-to-charge ratio (m/z) was compared.]]<html>
 +
<p> Results from Figure 4 and 5 indicate that hydrocarbons were successfully produced from <i>E. coli</i> that contained the PetroBrick construct, as analysed by GC-MS. In Figure 2, <i>E. coli</i> containing the PetroBrick had larger hydrocarbon peaks than the <i>E. coli</i> without the PetroBrick. Not only was the PetroBrick able to degrade NAs into alkanes, the PetroBrick could produce alkenes (Figure 3), indicating that the PetroBrick worked as expected! </p>
-
</html>[[File:Ucalgary_Decarboxylation_Alkanes_Alkenes_Results.png|center|700px|thumb|Figure 2: The alkane and alkene mass spectrums generated by analysis of hydrocarbons produced from E.coli containing the PetroBrick as in Figure 1, using naphthenic acids as a substrate, as measured with GC-MS. Relative intensity to mass to charge ratio were compared.]]<html>
 
-
<p></p>
+
<h2><i>Nocardia</i> Carboxylic Acid Reductase (CAR)- Can we do better?</h2>
-
<p> The above graphs indicate that hydrocarbons were successfully produced from E.coli that contained the PetroBrick plasmid, as analysed with GC-MS. In Figure 1, E.coli containing the PetroBrick had significantly higher hydrocarbon peaks than in a control of E.coli that did not contain the PetroBrick plasmid. Not only was the PetroBrick able to degrade naphthenic acids into alkanes, but it was also able to produce alkenes as shown by Figure 2, indicating that the PetroBrick had more potential than previously indicated. </p>
+
<p>Although we successfully used the PetroBrick to remove carboxyl groups from NAs, we wanted to improve on our results to get a higher yield and/or possibly target other compounds. One of our original concerns in using the PetroBrick to decarboyxlate NAs was that the first enzyme AAR only targeted fatty acids bound to ACP, and non-compatibility with NAs. Therefore, we searched for another enzyme carboxylic acid reductase (CAR) from <i>N. iowensis</i> known to perform a similar task as AAR - converting fatty acids to aldehydes, but with much lower specificity (He <i>et al</i>. 2004). Unlike AAR, CAR does not require covalent attachment to ACP, and likely to have broader substrate specificity.  The use of CAR did require a second gene from <i>N. iowensis</i> called <i>Nocardia</i> phosphopantetheinyl transferase (<i>npt</i>) to append a 4’- phosphopantetheine prosthetic group to CAR required for its full function (Venkitasubramanian <i>et al.</i>, 2006).</p>
 +
</html>[[File:Ucalgary Decarboxylation Team CAR Mechanism.jpg|center|700px|thumb|Figure 6: Mechanism of CAR catalysis. Taken from He <i>et al.</i>, 2004.]]<html>
-
<h3>Nocardia Carboxylic Acid Reductase (CAR)</h3>
+
<a name="OleT"></a><p>Another enzyme with the potential to remove carboxyl groups from NAs is olefin-forming fatty acid decarboxylase (<i><a href="http://partsregistry.org/Part:BBa_K902048:Experience">oleT</a></i>) from <i>Jeotgalicoccus</i> sp. ATCC 8456.  <i>OleT</i> of the cytochrome P450 family acts on fatty acids, but does have low substrate specificity (Rude <i>et al</i>. 2011).  Using <i>oleT</i> was beneficial because this single enzyme could do the job of the entire PetroBrick! Given that our decarboxylation approach was valid, we started testing and comparing <i>oleT</i> to the PetroBrick.</p>
-
<p>In order to model our part after the PetroBrick, an enzyme was needed to replace AAR that would not require covalent attachment to ACP and would have low enough specificity to accommodate diverse naphthenic acids. The enzyme chosen for this purpose was carboxylic acid reductase (CAR), found in Nocardia iowensis. CAR was selected for its remarkably low specificity in converting carboxylic acids to aldehydes. It was determined that a second gene from N. iowensis, called Nocardia phosphopantetheinyl transferase (NPT) was also necessary to append a 4’-phosphopantetheine prosthetic group to CAR required for its full function. </p>
+
<h2> Progress so far </h2>
-
<p>N. iowensis (NRRL 5646) was purchased from DSMZ and rehydrated, then grown in both solid and liquid brain heart infusion (BHI) media. CAR and NPT were successfully cloned out and amplified, and CAR was verified after ligation with the PET vector by a restriction digest and subsequent gel. NPT was likewise verified.</p>
+
<p>Genes <i>car</i> and <i>npt</i> were cloned from the host organism <i>N. iowensis</i> (NRRL 5646). <i>car</i> was ligated into the pET vector and verified by a restriction digest while <i>npt</i> was cloned into pSB1C3 (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902061">BBa_K902061</a>) and similarly verified.</p>
-
<p>CAR was also found to have six cut sites deemed illegal for BioBrick construction: one XpaI site, two EcoRI sites, and three NotI sites. These were first to be addressed by a multi-site mutagenesis derived from the QuikChange® Multi Site Directed Mutagenesis Kit, but this showed little success. Instead, a more time-consuming series of conventional single-site mutagenesis procedures was favoured, using the KAPA amplification system. A PET vector was chosen as an alternate vector to pSB1C3 to ligate with CAR for the duration of mutagenesis, while NPT was still ligated with pSB1C3. The XpaI and EcoRI sites were eliminated first, and following these steps and subsequent verification of their success, the mutated CAR+PET plasmid was successfully amplified with BioBrick primers after multiple attempts in preparation for the final construct. NPT was ligated in a construct following part J13002 from the iGEM parts registry, containing a ribosomal binding site and a TetR promoter.</p>
+
<p><i>car</i> was cloned into pET47b+ plasmid to remove six illegal cut-sites (one XbaI site, two EcoRI sites, and three NotI sites), as it was unsuitable for the BioBrick construction vectors. We first attempted to use a multi-site mutagenesis derived from the QuikChange<sup>®</sup> Multi-Site Directed Mutagenesis Kit, but had little success. Instead, a more time-consuming but effective series of conventional single-site <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis">mutagenesis procedure</a> was used with the KAPA Hi-Fi polymerase. The XbaI and EcoRI sites were eliminated first so that <i>car</i> can be moved from the pET Vector and ligated into the PSB1C3 vector (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902062">BBa_K902062</a>). 
-
<h3>How do the PetroBrick and CAR+NPT work together?</h3>
+
<p>The <i>oleT</i> was successfully amplified from the <i>Jeotgalicoccus</i> sp. ATCC 8456.
 +
<p> </p>
 +
<p>Like <i>car</i>, <i>oleT</i> was inserted in a pET47b+ (Novagen) vector before placing it into a BioBrick vector, as two illegal cut sites adjacent to one another needed to be mutagenized.  This part is now being ligated into pSB1C3.  We are currently in the process of constructing all three parts under control of a <i>tetR</i> promoter and ribosomal binding site (<a href="http://partsregistry.org/Part:BBa_J13002">BBa_J13002</a>), and then constructing these composite parts together as outlined below.</p>
-
<p>Our team decided to created a BioBrick construction containing three major parts. These included: the PetroBrick (as received from Washington), the CAR gene, and the NPT gene. This construction can be seen below.</p>
+
<h2>Final testing constructs</h2>
-
</html>[[File:Ucalgary_Decarboxylation_Team_J13002+car+J13002+npt+PetroBrick.png|center|500px]]<html>
+
<p>Final testing constructs are nearly complete.  These are illustrated in Figure 7 and will allow us to compare the three different approaches.  Unfortunately, Washington only sent us the PetroBrick and not the two individual components, we will have to compare a combination of the PetroBrick and <i>car/npt</i> to the PetroBrick alone and to <i>oleT</i>. </p>
-
<p>Both CAR and NPT use the part JI3002, which consists of pTetR (a constitutive promotor), as well as an RBS (ribosomal binding site). This constitutive promoter allows the gene to always be expressed, so that decarboxylation may consistently occur. The construction also includes Washington’s PetroBrick, which contributes the genes ADC and AAR. While AAR is useful to help convert some carboxylic acids and fatty acids to aldehydes, it is not known to be highly specific like the CAR enzyme. We are primarily interested in using the PetroBrick for its ADC gene, which is responsible for producing the only enzyme in our system that is capable of converting aldehydes into hydrocarbons. Meanwhile, both AAR and CAR in our construct will work to convert the initial carboxylic acids into the aldehydes required to produce hydrocarbons.</p>
+
<p></html>[[File:Ucalgary_Decarboxylation_Team_J13002+car+J13002+npt+PetroBrick.png|centre|600px]]<html>
 +
</html>[[File:Ucalgary Decarboxylation Team J13002+oleT.png|centre|280px|thumb|Figure 7: Final constructs required for validating and comparing different decarboxylation approaches]]<html></p>
-
</html>[[File:Ucalgary Decarboxylation Team CAR Mechanism.jpg|center|500px]]<html>
+
<a name="TestingOleT"></a><h2> Testing OleT </h2>
-
<h3>What about an alternative? (Jeotgalicoccus olefin-forming fatty acid decarboxylase, or OleT)</h3>
+
<p>One major stumbling block in testing out <i>oleT</i> is that it has been very difficult to ligate it into a vector, which has prevented us from submitting it as a BioBrick. As such, we chose to try some assays on the host organism:  <i>Jeotgalicoccus</i> sp. ATCC 8456.  This way we could at least validate that this gene was functional before we had our BioBricks.  We started by trying to verify the results by Rude <i>et al</i>., 2011, namely that OleT could convert fatty acids into alkenes.  We grew up cultures based on this <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oleT_in_Validation_Assay">protocol</a> and used GC-MS to analyze any alkene production (Figure 8 and 9).</p>
-
<p> In the early stages of work with CAR, an alternate approach to naphthenic acid decarboxylation was proposed that was entirely distinct from the PetroBrick+CAR/NPT system. The idea behind this method was to use olefin-forming fatty acid decarboxylase (OleT) from Jeotgalicoccus sp. ATCC 8456, a decarboxylase of the cytochrome P450 family acting on fatty acids, but with low substrate specificity. We chose to investigate OleT to determine if it was capable of directly decarboxylating naphthenic acids. </p>
+
<h2> Formation of alkanes by <i>Jeotgalicoccus</i> sp. ATCC 8456</h2>
-
 
+
-
<p> OleT was successfully amplified from the Jeotgalicoccus sp. ATCC 8456. Like CAR, OleT was inserted in a PET vector before placing it into a BioBrick, as two illegal cut sites adjacent to one another needed to be mutagenized. The final construct for OleT is very simple, containing the J13002 promotor/RBS, and the OleT gene. This simple construct should be able to convert carboxylic acids to terminal alkenes on its own. </p>
+
-
 
+
-
</html>[[File:Ucalgary Decarboxylation Team J13002+oleT.png|center|500px]]<html>
+
-
 
+
-
 
+
-
 
+
-
<h3>References</h3>
+
-
 
+
-
<p>https://www.dsmz.de/catalogues/details/culture/DSM-45197.html (retrieved 8/28/2012)</p>
+
-
 
+
-
<p>https://2011.igem.org/Team:Washington/Alkanes/Background (retrieved 8/28/2012)</p>
+
-
 
+
-
<p> http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025 (retrieved 8/28/2012)</p>
+
-
 
+
-
<p> He, A., Li, T., Daniels, L., Fotheringham, I., and Rosazza, J.P.N. 2004. Nocardia sp. Carboxylic Acid Reductase: Cloning, Expression, and Characterization of a New Aldehyde Oxidoreductase Family. Applied and Environmental Microbiology 70:1874–1881.</p>
+
-
 
+
-
<p> Venkitasubramanian, P., Daniels, L., and Rosazza, J.P.N. 2006. Reduction of Carboxylic Acids by Nocardia Aldehyde Oxidoreductase Requires a Phosphopantetheinylated Enzyme. Journal of Biological Chemistry 282:478-485. </p>
+
-
 
+
-
<p> Rude, M.A., Baron, T.S., Brubaker, S., Alibhai, M., Del Cardayre, S.B., and Schirmer, A. 2011. Terminal olefin (1-alkene) biosynthesis by a novel p450 fatty acid decarboxylase from Jeotgalicoccus species. Applied and Environmental Microbiology 77:1718–1727.</p>
+
 +
</html>[[File:UofC_OleT_Assay_1.png|centre|700px|thumb|Figure 8.  Gas chromatograph demonstrating the production of olefins (alkenes) from fatty acids as shown from the increase in the peak with a retention time of 14.7 min.  The dramatic change in peak intensity at this point suggests that we are producing hydrocarbons.]]
 +
[[File:UofC_OleT_2nd_Assay.png|centre|700px|thumb|Figure 9. Mass spectrum of the peak in Figure 8 at retention time 14.7 min.  Demonstrating that this peak is an olefin, which is known to be produced in <i>Jeotgalicoccus</i>.  This verifies our proof-of-concept that the <i>Jeotgalicoccus</i> species can degrade fatty acids into olefins. ]]<html>
 +
<p>Based on the additional peak we saw in the gas chromatograph, we could show that our <i>E. coli</i> can produce alkenes with the <i>oleT</i>.  This is may be an improvement over the PetroBrick since OleT is only one enzyme instead of two; however, future testing is still needed. Now that we have validated the function of OleT in producing alkenes, the next step is to test it out on complex naphthenic acids in order to compare it to the PetroBrick. This testing is still underway.</p>
</html>
</html>
-
 
+
}}
}}

Latest revision as of 02:05, 27 October 2012

Hello! iGEM Calgary's wiki functions best with Javascript enabled, especially for mobile devices. We recommend that you enable Javascript on your device for the best wiki-viewing experience. Thanks!

Decarboxylation

Why Decarboxylation?

Among the toxins found in the tailing ponds, naphthenic acids (NAs) are among the most harmful and the most common. Though there is great diversity within the NAs class of compounds, all share the common chemical feature of a carboxylic acid group. The carboxyl group is the primary cause for their toxicity, allowing these chemicals to traverse cell membranes and react with cellular materials (Frank et al. 2009). NAs are recalcitrant (not easily degraded), potentially harmful to the surrounding ecosystem (Clemente & Fedorak, 2005) and corrosive to extraction and transport equipment of petroleum materials (Slavcheva et al. 1999). Corrosion of pipelines leads to higher maintenance costs as well as the grim possibility of these and other toxins leaking into the environment. There is a need for methods to degrade NAs that are not prohibitively expensive or that would result in production of other hazardous chemicals.

The main goal of OSCAR is to turn toxins like these into useable hydrocarbons by removing the carboxylic acid group(s) (Behar & Albrecht, 1984). Since NAs from petroleum deposits are a variable mixture, an enzymatic process with broad specificity is necessary. With the removal of the carboxylic acid moiety, we aim to produce alkanes suitable for use as fuel. The goal of this subproject was to find one or more suitable pathways to accomplish the decarboxylation of compounds such as NAs with the broadest specificity.

The PetroBrick

The 2011 Washington iGEM team developed the PetroBrick (BBa_K590025.), a BioBrick consisting of two primary genes. These include acyl-ACP reductase (AAR), which reduces fatty acids bound to ACP to fatty aldehydes, and a second gene called aldehyde decarbonylase (ADC), which subsequently cleaves the entire aldehyde group and results in a hydrocarbon chain (Sukovich, 2010). Essentially this allows for hydrocarbons to be produced from glucose. What we realized though, is that the fatty acids that the PetroBrick targets, have a very similar structure to NAs.

Figure 1: A comparison of the structure of fatty acids and naphthenic acids

We predicted that the PetroBrick may have the potential to turn NAs in to hydrocarbons and be a perfect solution to remediating NAs! First though, we needed to show that the PetroBrick did in fact work as expected. We had some difficulty with the DNA from the registry and had to request the constructs directly from the Washington team. Once we had the PetroBrick, we needed to verify that the PetroBrick would work in our hands as it did for the 2011 Washington team. Figures 2 and 3 demonstrate the function of the PetroBrick.

Figure 2: Gas chromatograph of the differences in peak composition between an E. coli control and the PetroBrick. There was a large increase in a peak with a retention time of 12.25 min, suggesting that the PetroBrick was producing a new hydrocarbon compound.
Figure 3: Mass spectrum of the gas chromatograph peak at 12.25 min. This spectra suggests that the PetroBrick is selectively producing a C15 alkane, which resembles the results from the Washington 2011 iGEM team.

With the PetroBrick able to successfully produce alkanes, we next wanted to test the PetroBrick on NAs to see if they could be selectively converted into alkanes! This experiment used commercial NA fractions, which included a large number of different complex NA compounds.

Successful conversion of NAs into hydrocarbons!

Figure 4: The relative intensity of alkane production from NAs as measured with a GC-MS in E. coli with and without the PetroBrick. A concentrated NA standard was included for comparison of peaks.
Figure 5: Mass spectra of alkanes and alkenes produced from NAs with E. coli containing the PetroBrick as in Figure 2. Relative intensity of mass-to-charge ratio (m/z) was compared.

Results from Figure 4 and 5 indicate that hydrocarbons were successfully produced from E. coli that contained the PetroBrick construct, as analysed by GC-MS. In Figure 2, E. coli containing the PetroBrick had larger hydrocarbon peaks than the E. coli without the PetroBrick. Not only was the PetroBrick able to degrade NAs into alkanes, the PetroBrick could produce alkenes (Figure 3), indicating that the PetroBrick worked as expected!

Nocardia Carboxylic Acid Reductase (CAR)- Can we do better?

Although we successfully used the PetroBrick to remove carboxyl groups from NAs, we wanted to improve on our results to get a higher yield and/or possibly target other compounds. One of our original concerns in using the PetroBrick to decarboyxlate NAs was that the first enzyme AAR only targeted fatty acids bound to ACP, and non-compatibility with NAs. Therefore, we searched for another enzyme carboxylic acid reductase (CAR) from N. iowensis known to perform a similar task as AAR - converting fatty acids to aldehydes, but with much lower specificity (He et al. 2004). Unlike AAR, CAR does not require covalent attachment to ACP, and likely to have broader substrate specificity. The use of CAR did require a second gene from N. iowensis called Nocardia phosphopantetheinyl transferase (npt) to append a 4’- phosphopantetheine prosthetic group to CAR required for its full function (Venkitasubramanian et al., 2006).

Figure 6: Mechanism of CAR catalysis. Taken from He et al., 2004.

Another enzyme with the potential to remove carboxyl groups from NAs is olefin-forming fatty acid decarboxylase (oleT) from Jeotgalicoccus sp. ATCC 8456. OleT of the cytochrome P450 family acts on fatty acids, but does have low substrate specificity (Rude et al. 2011). Using oleT was beneficial because this single enzyme could do the job of the entire PetroBrick! Given that our decarboxylation approach was valid, we started testing and comparing oleT to the PetroBrick.

Progress so far

Genes car and npt were cloned from the host organism N. iowensis (NRRL 5646). car was ligated into the pET vector and verified by a restriction digest while npt was cloned into pSB1C3 (BBa_K902061) and similarly verified.

car was cloned into pET47b+ plasmid to remove six illegal cut-sites (one XbaI site, two EcoRI sites, and three NotI sites), as it was unsuitable for the BioBrick construction vectors. We first attempted to use a multi-site mutagenesis derived from the QuikChange® Multi-Site Directed Mutagenesis Kit, but had little success. Instead, a more time-consuming but effective series of conventional single-site mutagenesis procedure was used with the KAPA Hi-Fi polymerase. The XbaI and EcoRI sites were eliminated first so that car can be moved from the pET Vector and ligated into the PSB1C3 vector (BBa_K902062).

The oleT was successfully amplified from the Jeotgalicoccus sp. ATCC 8456.

Like car, oleT was inserted in a pET47b+ (Novagen) vector before placing it into a BioBrick vector, as two illegal cut sites adjacent to one another needed to be mutagenized. This part is now being ligated into pSB1C3. We are currently in the process of constructing all three parts under control of a tetR promoter and ribosomal binding site (BBa_J13002), and then constructing these composite parts together as outlined below.

Final testing constructs

Final testing constructs are nearly complete. These are illustrated in Figure 7 and will allow us to compare the three different approaches. Unfortunately, Washington only sent us the PetroBrick and not the two individual components, we will have to compare a combination of the PetroBrick and car/npt to the PetroBrick alone and to oleT.

Ucalgary Decarboxylation Team J13002+car+J13002+npt+PetroBrick.png
Figure 7: Final constructs required for validating and comparing different decarboxylation approaches

Testing OleT

One major stumbling block in testing out oleT is that it has been very difficult to ligate it into a vector, which has prevented us from submitting it as a BioBrick. As such, we chose to try some assays on the host organism: Jeotgalicoccus sp. ATCC 8456. This way we could at least validate that this gene was functional before we had our BioBricks. We started by trying to verify the results by Rude et al., 2011, namely that OleT could convert fatty acids into alkenes. We grew up cultures based on this protocol and used GC-MS to analyze any alkene production (Figure 8 and 9).

Formation of alkanes by Jeotgalicoccus sp. ATCC 8456

Figure 8. Gas chromatograph demonstrating the production of olefins (alkenes) from fatty acids as shown from the increase in the peak with a retention time of 14.7 min. The dramatic change in peak intensity at this point suggests that we are producing hydrocarbons.
Figure 9. Mass spectrum of the peak in Figure 8 at retention time 14.7 min. Demonstrating that this peak is an olefin, which is known to be produced in Jeotgalicoccus. This verifies our proof-of-concept that the Jeotgalicoccus species can degrade fatty acids into olefins.

Based on the additional peak we saw in the gas chromatograph, we could show that our E. coli can produce alkenes with the oleT. This is may be an improvement over the PetroBrick since OleT is only one enzyme instead of two; however, future testing is still needed. Now that we have validated the function of OleT in producing alkenes, the next step is to test it out on complex naphthenic acids in order to compare it to the PetroBrick. This testing is still underway.