Difference between revisions of "Team:Bordeaux/Design"

 
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     <!-- Intro Team IGEM-->
 
     <!-- Intro Team IGEM-->
 
     <div class="container text_intro">
 
     <div class="container text_intro">
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         <h2>Design</h2>
+
         <h1 class="text-longshadow">Design</h1>
 
         <p> Recent studies have shown that multiple organisms have the ability of metabolizing 5-hydroxymethylfurfural (HMF).
 
         <p> Recent studies have shown that multiple organisms have the ability of metabolizing 5-hydroxymethylfurfural (HMF).
 
             For instance, enzyme able to oxidize HMF into Furan-2,5-dicarboxylic acid (FDCA) has been discovered in fungal
 
             For instance, enzyme able to oxidize HMF into Furan-2,5-dicarboxylic acid (FDCA) has been discovered in fungal
−
             species such as Caldariomyces fumago [1] or in prokaryotic species Cupriavidus basilensis (C. basilensis) [2].
+
             species such as
−
             and Methylovorus sp. [4].</p>
+
            <i>Caldariomyces fumago</i> [1] or in prokaryotic species
−
         <p>As we intended to work with Escherichia coli (E. coli), we focused on the enzymes discovered in prokaryotes. Due
+
            <i>Cupriavidus basilensis (C. basilensis)</i> [2]. and
−
            to glycosylations on the enzymes that has been found in Caldaryomyces fumago and Eukaryotes/Prokaryotes gene
+
             <i>Methylovorus sp.</i> [4].</p>
−
            compatibility issue, fungal enzymes have been dismissed. The following section describes the enzymes selected
+
         <p>As we intended to work with
−
            to achieve an efficient transformation of HMF into FDCA.
+
            <i>Escherichia coli (E. coli)</i>, we focused on the enzymes discovered in prokaryotes. Due to glycosylations on
 +
            the enzymes that has been found in
 +
            <i>Caldaryomyces fumago</i> and Eukaryotes/Prokaryotes gene compatibility issue, fungal enzymes have been dismissed.
 +
            The following section describes the enzymes selected to achieve an efficient transformation of HMF into FDCA.
 
         </p>
 
         </p>
−
         <p>HmfH is an enzyme that has been discovered in C. basilensis. This enzyme is part of a gene cluster implied in furanic
+
         <p>HmfH is an enzyme that has been discovered in
−
            compound degradation. HmfH homologues as also been found in several other bacterial species [6]. In a study,
+
            <i>C. basilensis</i>. This enzyme is part of a gene cluster implied in furanic compound degradation. HmfH homologues
−
            HmfH gene has been cloned into Pseudomonas putida in order to enable this bacteria to synthetize FDCA from HMF.
+
            has also been found in several other bacterial species [6]. In a study, HmfH gene has been cloned into
−
            HmfH catalyse two successive oxidations that transform HMF into 5-(hydroxymethyl)furoic acid ( HMF acid) and
+
            <i>Pseudomonas putida</i> in order to enable this bacteria to synthetize FDCA from HMF. HmfH catalyse two successive
−
            then into FDCA [5] ( fig 2. ). The modified P. putida with HmfH was able to produce FDCA without excessive amount
+
            oxidations that transform HMF into 5-(hydroxymethyl)furoic acid ( HMF acid) and then into FDCA [5] ( fig 2. ).
−
            of other furan derivatives. One issue with this enzyme is that the second oxidation of HMF acid into FDCA is
+
            The modified
−
            slower than the first one. It results in the accumulation of the intermediate product, HMF acid. In fed batch
+
            <i>P. putida</i> with HmfH was able to produce FDCA without excessive amount of other furan derivatives. One issue
−
            culture the accumulation of intermediate product could lead to efficiency issue to the production of high purity
+
            with this enzyme is that the second oxidation of HMF acid into FDCA is slower than the first one. It results
−
            FDCA.
+
            in the accumulation of the intermediate product, HMF acid. In fed batch culture the accumulation of intermediate
 +
            product could lead to an efficient production of high pure FDCA.
 
         </p>
 
         </p>
 
         <p>One way to compensate for that is to add other enzymes to the artificial metabolic pathway, in order to speed up
 
         <p>One way to compensate for that is to add other enzymes to the artificial metabolic pathway, in order to speed up
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             HMF into FDCA with HMF acid as a reaction intermediate. The Kcat of this enzyme on 5-HMF has been estimated to
 
             HMF into FDCA with HMF acid as a reaction intermediate. The Kcat of this enzyme on 5-HMF has been estimated to
 
             5.1 mM-1.min-1 [8]. By acting synergically with HmfH, Aldh1 could limit the accumulation of HmfAcid.</p>
 
             5.1 mM-1.min-1 [8]. By acting synergically with HmfH, Aldh1 could limit the accumulation of HmfAcid.</p>
 +
        <figure class="figure">
 +
            <img src="https://static.igem.org/mediawiki/2018/1/1f/T--Bordeaux--HmfO.png" class="figure-img img-fluid rounded" alt="HmfO protein structure">
 +
            <figcaption class="figure-caption">HmfO protein structure</figcaption>
 +
        </figure>
 
         <p>An other enzyme that may turn worthwhile for the biosynthesis of FDCA is HmfO (5-(hydroxymethyl)furfural Oxydase).
 
         <p>An other enzyme that may turn worthwhile for the biosynthesis of FDCA is HmfO (5-(hydroxymethyl)furfural Oxydase).
−
             This enzyme is present in Methylovorus sp. and in C. basilensis. HmfO belongs to a C. basilensis HMF14 gene cluster
+
             This enzyme is present in
−
            involved in Hmf degradation pathway. HmfO and HmfH are homologous, they both belongs to the GMC (glucose-methanol-choline)
+
            <i>Methylovorus sp.</i> and in
−
            oxidoreductase proteins family. The N-ter GMC domain bind to FAD, and release H2O2 as a byproduct [4]. However,
+
            <i>C. basilensis</i>. HmfO belongs to a
−
            unlike HmfH , HmfO needs three successive oxidations of HMF to reach FDCA (fig 1.). Thereby two intermediary
+
            <i> C. basilensis</i> HMF14 gene cluster involved in Hmf degradation pathway. HmfO and HmfH are homologous, they
−
            compounds are formed, 2,5-Furandicarboxaldehyde (furfural) (DFF) and 5-formyl-2-furancarboxylic acid (FFA) [4].</p>
+
            both belongs to the GMC (glucose-methanol-choline) oxidoreductase proteins family. The N-ter GMC domain bind
 +
            to FAD, and release H2O2 as a byproduct [4]. However, unlike HmfH , HmfO needs three successive oxidations of
 +
            HMF to reach FDCA (fig 1.). Thereby two intermediary compounds are formed, 2,5-Furandicarboxaldehyde (furfural)
 +
            (DFF) and 5-formyl-2-furancarboxylic acid (FFA) [4].</p>
 +
        <figure class="figure">
 +
            <img src=" https://static.igem.org/mediawiki/2018/4/46/T--Bordeaux--HMF-FDCA.png" class="figure-img img-fluid rounded" alt="Fig 2. Artificial metabolic pathway of oxidation of HMF into FDCA, using HmfH,HmfO and Aldh1 enzyms. Oxydation reactions
 +
            imply the use of a FAD co-factor and the release of hydrogen peroxyde.">
 +
            <figcaption class="figure-caption">Artificial metabolic pathway of oxidation of HMF into FDCA, using HmfH,HmfO and Aldh1 enzyms. Oxydation reactions
 +
                imply the use of a FAD co-factor and the release of hydrogen peroxyde.</figcaption>
 +
        </figure>
 
         <p>In order to obtain an efficient whole cell biocatalyst genes coding for the three previously described enzymes have
 
         <p>In order to obtain an efficient whole cell biocatalyst genes coding for the three previously described enzymes have
 
             to be under control of a strong promoter. To maximize the expression of these proteins it was planned to put
 
             to be under control of a strong promoter. To maximize the expression of these proteins it was planned to put
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             phase quicker it was planned to use an inducible promoter.The part pBAD strong (BBa_K206000) , registered by
 
             phase quicker it was planned to use an inducible promoter.The part pBAD strong (BBa_K206000) , registered by
 
             iGEM09_British_Columbia, offer a high expression level.</p>
 
             iGEM09_British_Columbia, offer a high expression level.</p>
−
         <p>In order to study each proteins activity individually, it was planned to cloned each one of them in pSB1-C3 under
+
         <p>In order to study each proteins activity individually, it was planned to clone each one of them in pSB1-C3 under
−
             control of BBa_K608002 (“strong promoter strong RBS”). Moreover , so as to study their joint activity, an operon
+
             control of BBa_K608002 (“strong promoter strong RBS”). Moreover, to study their joint activity, an operon structure
−
             structure of HmfH, HmfO and Aldh1 under control of an constitutive and inducible promoter has been designed (fig
+
             of HmfH, HmfO and Aldh1 under control of an constitutive and inducible promoter has been designed (fig 3).
−
            3).
+
 
         </p>
 
         </p>
 +
        <img src="https://static.igem.org/mediawiki/2018/0/0a/T--Bordeaux--mainplasmid.png" class="col-12 img-fluid">
 +
        <p>See standards biobrick constructions below (click to view it fullscreen)</p>
 +
        <div class="row col-12" style="margin-bottom: 50px; margin-top: 50px; text-align: center!important">
 +
            <a href="https://static.igem.org/mediawiki/2018/6/6d/T--Bordeaux--stdbiobrick1.png" class="col-4" target="_blank">
 +
                <img src="https://static.igem.org/mediawiki/2018/6/6d/T--Bordeaux--stdbiobrick1.png" class="img-fluid">
 +
                <p style="text-align: center">pSB1C3 + Aldh1 (Standard BioBrick)</p>
 +
            </a>
 +
            <a href="https://static.igem.org/mediawiki/2018/a/af/T--Bordeaux--stdbiobrick2.png" class="col-4" target="_blank">
 +
                <img src="https://static.igem.org/mediawiki/2018/a/af/T--Bordeaux--stdbiobrick2.png" class="img-fluid">
 +
                <p style="text-align: center">pSB1C3 + HmfH (Standard BioBrick)</p>
 +
            </a>
 +
            <a href="https://static.igem.org/mediawiki/2018/a/a3/T--Bordeaux--stdbiobrick3.png" class="col-4" target="_blank">
 +
                <img src="https://static.igem.org/mediawiki/2018/a/a3/T--Bordeaux--stdbiobrick3.png" class="img-fluid">
 +
                <p style="text-align: center">pSB1C3 + HmfO (Standard BioBrick)</p>
 +
            </a>
 +
        </div>
 
         <div id="ref">
 
         <div id="ref">
 
             <h4>References :</h4>
 
             <h4>References :</h4>
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                     D.E., Fraaije M.W.
 
                     D.E., Fraaije M.W.
 
                 </li>
 
                 </li>
−
                 <li>"Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688."
+
                 <li>"Discovery and characterization of a 5-hydroxymethylfurfural oxidase from
−
                    Dijkman W.P., Fraaije M.W.
+
                    <i>Methylovorus sp.</i> strain MP688." Dijkman W.P., Fraaije M.W.
 
                 </li>
 
                 </li>
 
                 <li>2010 Aug;101(16):6291-6. doi: 10.1016/j.biortech.2010.03.050. Epub 2010 Apr 3. Efficient whole-cell biotransformation
 
                 <li>2010 Aug;101(16):6291-6. doi: 10.1016/j.biortech.2010.03.050. Epub 2010 Apr 3. Efficient whole-cell biotransformation
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Latest revision as of 09:59, 16 October 2018

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Design

Recent studies have shown that multiple organisms have the ability of metabolizing 5-hydroxymethylfurfural (HMF). For instance, enzyme able to oxidize HMF into Furan-2,5-dicarboxylic acid (FDCA) has been discovered in fungal species such as Caldariomyces fumago [1] or in prokaryotic species Cupriavidus basilensis (C. basilensis) [2]. and Methylovorus sp. [4].

As we intended to work with Escherichia coli (E. coli), we focused on the enzymes discovered in prokaryotes. Due to glycosylations on the enzymes that has been found in Caldaryomyces fumago and Eukaryotes/Prokaryotes gene compatibility issue, fungal enzymes have been dismissed. The following section describes the enzymes selected to achieve an efficient transformation of HMF into FDCA.

HmfH is an enzyme that has been discovered in C. basilensis. This enzyme is part of a gene cluster implied in furanic compound degradation. HmfH homologues has also been found in several other bacterial species [6]. In a study, HmfH gene has been cloned into Pseudomonas putida in order to enable this bacteria to synthetize FDCA from HMF. HmfH catalyse two successive oxidations that transform HMF into 5-(hydroxymethyl)furoic acid ( HMF acid) and then into FDCA [5] ( fig 2. ). The modified P. putida with HmfH was able to produce FDCA without excessive amount of other furan derivatives. One issue with this enzyme is that the second oxidation of HMF acid into FDCA is slower than the first one. It results in the accumulation of the intermediate product, HMF acid. In fed batch culture the accumulation of intermediate product could lead to an efficient production of high pure FDCA.

One way to compensate for that is to add other enzymes to the artificial metabolic pathway, in order to speed up the second oxidation of HMF acid into FDCA.

An enzyme of interest, HMF dehydrogenase (Aldh1), is found to catalyse identical reaction as HmfH. This enzyme oxidizes HMF into FDCA with HMF acid as a reaction intermediate. The Kcat of this enzyme on 5-HMF has been estimated to 5.1 mM-1.min-1 [8]. By acting synergically with HmfH, Aldh1 could limit the accumulation of HmfAcid.

HmfO protein structure
HmfO protein structure

An other enzyme that may turn worthwhile for the biosynthesis of FDCA is HmfO (5-(hydroxymethyl)furfural Oxydase). This enzyme is present in Methylovorus sp. and in C. basilensis. HmfO belongs to a C. basilensis HMF14 gene cluster involved in Hmf degradation pathway. HmfO and HmfH are homologous, they both belongs to the GMC (glucose-methanol-choline) oxidoreductase proteins family. The N-ter GMC domain bind to FAD, and release H2O2 as a byproduct [4]. However, unlike HmfH , HmfO needs three successive oxidations of HMF to reach FDCA (fig 1.). Thereby two intermediary compounds are formed, 2,5-Furandicarboxaldehyde (furfural) (DFF) and 5-formyl-2-furancarboxylic acid (FFA) [4].

Fig 2. Artificial metabolic pathway of oxidation of HMF into FDCA, using HmfH,HmfO and Aldh1 enzyms. Oxydation reactions imply the use of a FAD co-factor and the release of hydrogen peroxyde.
Artificial metabolic pathway of oxidation of HMF into FDCA, using HmfH,HmfO and Aldh1 enzyms. Oxydation reactions imply the use of a FAD co-factor and the release of hydrogen peroxyde.

In order to obtain an efficient whole cell biocatalyst genes coding for the three previously described enzymes have to be under control of a strong promoter. To maximize the expression of these proteins it was planned to put them under control of promoter improved by freiburg 2011 iGem team and characterized by Slovenia HS 2015 iGem team (BBa_K608002).

Genes overexpression could be a drag on bacterial growth. In order to able bacterial culture to reach stationary phase quicker it was planned to use an inducible promoter.The part pBAD strong (BBa_K206000) , registered by iGEM09_British_Columbia, offer a high expression level.

In order to study each proteins activity individually, it was planned to clone each one of them in pSB1-C3 under control of BBa_K608002 (“strong promoter strong RBS”). Moreover, to study their joint activity, an operon structure of HmfH, HmfO and Aldh1 under control of an constitutive and inducible promoter has been designed (fig 3).

See standards biobrick constructions below (click to view it fullscreen)

pSB1C3 + Aldh1 (Standard BioBrick)

pSB1C3 + HmfH (Standard BioBrick)

pSB1C3 + HmfO (Standard BioBrick)

References :

  1. 5-hydroxymethylfurfural conversion by fungal aryl-alcohol oxidase and unspecific peroxygenase Juan Carro, Patricia Ferreira, Leonor Rodrıguez, Alicia Prieto, Ana Serrano, Beatriz Balcells, Ana Arda, Jesus Jim enez-Barbero, Ana Gutierrez, Rene Ullrich, Martin Hofrichter and Angel T. Martınez
  2. Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14. Koopman F, Wierckx N, de Winde JH, Ruijssenaars HJ.
  3. "Enzyme-catalyzed oxidation of 5-hydroxymethylfurfural to furan-2,5-dicarboxylic acid." Dijkman W.P., Groothuis D.E., Fraaije M.W.
  4. "Discovery and characterization of a 5-hydroxymethylfurfural oxidase from Methylovorus sp. strain MP688." Dijkman W.P., Fraaije M.W.
  5. 2010 Aug;101(16):6291-6. doi: 10.1016/j.biortech.2010.03.050. Epub 2010 Apr 3. Efficient whole-cell biotransformation of 5-(hydroxymethyl)furfural into FDCA, 2,5-furandicarboxylic acid. Koopman F1, Wierckx N, de Winde JH, Ruijssenaars HJ.
  6. Microbial degradation of furanic compounds: biochemistry, genetics, and impact ; Nick Wierckx, Frank Koopman, Harald J. Ruijssenaars, and Johannes H. de Winde
  7. Inhibition performance of lignocellulose degradation products on industrial cellulase enzymes during cellulose hydrolysis. Jing X, Zhang X, Bao J.
  8. Metabolic engineering of Raoultella ornithinolytica BF60 for the production of 2, 5- 2 furandicarboxylic acid from 5-hydroxymethylfurfural Gazi Sakir Hossain, Haibo Yuan, Jianghua Li, Hyun-dong Shin, Miao Wang, Guocheng Du, Jian Chen, Long Liu