Team:UESTC-China/Modeling1

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<a href="https://2014.igem.org/Team:UESTC-China/Modeling1"><li>HPS/PHI</li></a>
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  <h1 style="color:#1b1b1b; position:relative; left:0px; padding:15 5px; font-size:35px; font-family: calibri, arial, helvetica, sans-serif; font-weight: bold;font-style: Italic; text-align:center; width:1140px;">Photosynthetic HCHO assimilation pathway</h1>
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  <h1 style="color:#1b1b1b; position:relative; left:0px; padding:15 5px; font-size:35px; font-family: calibri, arial, helvetica, sans-serif; font-weight: bold;font-style: Italic; text-align:center; width:1140px;">Photosynthetic formaldehyde assimilation pathway</h1>
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  <h1 class="SectionTitles" style="text-align:left; width:500px;">Mathematical Principles</h1>
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  <h1 class="SectionTitles" style=" width:1100px;">Mathematical principles</h1>
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<p style="color:#1b1b1b;">Almost all chemical reactions obey the law of constant proportion:</p>
<p style="color:#1b1b1b;">Almost all chemical reactions obey the law of constant proportion:</p>
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  <h1 class="SectionTitles" style="text-align:left; width:500px;">Photosynthetic HCHO assimilation pathway</h1>
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  <h1 class="SectionTitles" style=" width:1100px;">Photosynthetic formaldehyde assimilation pathway</h1>
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<p style="color:#1b1b1b;">The metabolism of photosynthetic HCHO assimilation was shown on Fig.1. Since the substrate (Ru5P) and product (F6P) of the sequential reactions catalyzed by HPS and PHI are intermediates of the Calvin cycle in plants, photosynthesis could provide sufficient substrates for the reactions catalyzed by HPS and PHI if the two enzymes were expressed in plant <i>(Song, Orita et al. 2010)</i>. It has been proved that over-expressing the HPS/PHI fusion protein can enhance the ability of the plants to absorb and assimilate exogenous HCHO <i>(Chen, Yurimoto et al. 2010)</i>. In this case, we utilize the mathematical principles described above to analyze the metabolism.</p>
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<p style="color:#1b1b1b;">The metabolism of photosynthetic formaldehyde assimilation was shown on Fig.1. Since the substrate (Ru5P) and product (F6P) of the sequential reactions catalyzed by HPS and PHI are intermediates of the Calvin cycle in plants, photosynthesis could provide sufficient substrates for the reactions catalyzed by HPS and PHI if the two enzymes were expressed in plant <i>(Song et al., 2010)</i>. It has been proved that over-expressing the HPS/PHI fusion protein can enhance the ability of the plants to absorb and assimilate exogenous formaldehyde <i>(Chen et al., 2010)</i>. In this case, we utilize the mathematical principles described above to analyze the metabolism.</p>
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<strong>Fig.1</strong> Schematic diagram of photosynthetic formaldehyde assimilation pathway. Ru5P, D-ribulose 5-phosphate; Hu6P, D-arabino-3-hexulose 6-phosphate; F6P, fructose 6-phosphate; Xu5P, xylulose 5-phosphate; RuBP, ribulose 1,5-bisphosphate; 3-PGA, glycerate 3-phosphate; FBP, fructose-1,6-bisphosphatase;
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<p style="position:relative; left:0px; padding:15 5px; font-size:20px; font-family: calibri, arial, helvetica, sans-serif; font-style: Italic; text-align:left; width:650px; color:#1b1b1b;"><strong>Fig.1</strong> Schematic diagram of photosynthetic HCHO assimilation pathway. Ru5P, D-ribulose 5-phosphate; Hu6P, D-arabino-3-hexulose 6-phosphate; F6P, fructose 6-phosphate; Xu5P, xylulose 5-phosphate; RuBP, ribulose 1,5-bisphosphate; 3-PGA, glycerate 3-phosphate; FBP, fructose-1,6-bisphosphatase;</p>
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<p style="color:#1b1b1b;">Simplify the system (Fig.2), consist of the input of formaldehyde and CO2, the recycle of Ru5P and the output of F6P:</p>
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<p style="color:#1b1b1b;">Simplify the system (Fig.2), consist of the input of HCHO and CO2, the recycle of Ru5P and the output of F6P:</p>
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<p style="position:relative; left:0px; padding:15 5px; font-size:20px; font-family: calibri, arial, helvetica, sans-serif; font-style: Italic; text-align:left; width:740px; color:#1b1b1b;"><strong>Fig.2</strong> A simplified version of photosynthetic HCHO assimilation pathway</p>
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<strong>Fig.2</strong> A simplified version of photosynthetic HCHO assimilation pathway
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<p style="color:#1b1b1b;">The mechanism of this system can be represented by a set of chemical reactions, as shown below.</p>
<p style="color:#1b1b1b;">The mechanism of this system can be represented by a set of chemical reactions, as shown below.</p>
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[C0]: the initial concentration of formaldehyde.
[C0]: the initial concentration of formaldehyde.
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<h1 class="SectionTitles" style="width:1100px;">Results</h1>
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<p style="color:#1b1b1b;">By changing the value of those parameters (<i>k1, k2</i> … ), we obtained the relationship (Fig.3) between the concentration of different components (Ru5P, F6P and HCHO) versus the time. </p>
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<p style="color:#1b1b1b;">By changing the value of those parameters (<i>k1, k2</i> … ), we obtained the relationship (Fig.3) between the concentration of different components (Ru5P, F6P and formaldehyde) versus the time. </p>
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<strong>Fig.3</strong> The diagram of concentration versus time. A for Ru5P and F6P, B for HCHO and C for those three components
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<p style="color:#1b1b1b;">From Fig.3, we found that the components tend to be the steady state when time goes by. Means that when the formaldehyde absorbed into the plant cell, the original steady state would be broken, but after a period of time, the cells will restore homeostasis which indicated that the indoor formaldehyde has been absorbed by the plant. For figure 3B, in the initial stage, formaldehydewill continue to grow due to the delayed effects of reaction; subsequently,the concentration of formaldehyde begins to decrease with time and finally tends to be the steady state.</p>
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<p style="position:relative; left:0px; padding:15 5px; font-size:20px; font-family: calibri, arial, helvetica, sans-serif; font-style: Italic; text-align:left; width:1000px; color:#1b1b1b;"><strong>Fig.3</strong> The diagram of concentration versus time. A for Ru5P and F6P, B for HCHO and C for those three components</p>
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<h1 class="SectionTitles" style=" width:1100px;">Link to other modeling</h1>
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<a href="https://2014.igem.org/Team:UESTC-China/Modeling2" class="button">Folate-independent pathway</a>
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<a href="https://2014.igem.org/Team:UESTC-China/Modeling3" class="button">Modeling of stoma</a>
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<p style="color:#1b1b1b;">From Fig.3, we found that the components tend to be the steady state when time goes by. Means that when the formaldehyde into the plant cell, the original steady state would be broken, but after a period of time, the cells will restore homeostasis which indicated that the indoor formaldehyde has been absorbed by the plant. For figure 3B, in the initial stage, formaldehydewill continue to grow due to the delayed effects of reaction; subsequently,the concentration of formaldehyde begins to decrease with time and finally tends to be the steady state.</p>
 
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<a href="https://2014.igem.org/Team:UESTC-China/Modeling2" class="button">FALDH/FDH</a>
 
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<h1 class="SectionTitles" style="width:1100px;">Reference</h1>
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<p style="position:relative; left:0px; padding:15 5px; font-size:20px; font-family: calibri, arial, helvetica, sans-serif; font-style: Italic; text-align:justify; color:#1b1b1b;">Chen, L. M., H. Yurimoto, K. Z. Li, I. Orita, M. Akita, N. Kato, Y. Sakai and K. Izui (2010). "Assimilation of formaldehyde in transgenic plants due to the introduction of the bacterial ribulose monophosphate pathway genes." <b>Biosci Biotechnol Biochem</b> 74(3): 627-635.</p>
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<p style="position:relative; left:0px; padding:15 5px; font-size:20px; font-family: calibri, arial, helvetica, sans-serif; font-style: Italic; text-align:justify; color:#1b1b1b;">Song, Z., I. Orita, F. Yin, H. Yurimoto, N. Kato, Y. Sakai, K. Izui, K. Li and L. Chen (2010). "Overexpression of an HPS/PHI fusion enzyme from Mycobacterium gastri in chloroplasts of geranium enhances its ability to assimilate and phytoremediate formaldehyde." <b>Biotechnol Lett</b> 32(10): 1541-1548.</p>
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Latest revision as of 01:55, 18 October 2014

UESTC-China