Team:Edinburgh/Biorefinery

From 2011.igem.org

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We can use '''stuff''' to break down stuff and then use other stuff to create new stuff with this stuff.
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Yassen will do this bit!
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Once we have glucose, the natural product of cellulose degradation, possible products we can make are:
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* Levan
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** Levan can be used in foods, feeds, cosmetics, and the pharmaceutical and chemical industry. However limitations exist. Weak chemical stability and purification are problems. Once they are solved, the market for this should be very high.
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*** How to make levan is so far a mystery!
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* Ethanol
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** If the goal is to produce low yield high value, then ethanol is probably not the best option. There is sustainable issues which arise from making ethanol from biomass etc.
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* Isoprene
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* High Fructose Corn Syrup
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** Xylose isomerase is the enzyme used in industry to break down glucose into fructose. It catalyses the chemical reaction D-xylose into D-xylulose. (Part not available in registry). However there has been talk on UK and EU level of banning HFCS. It has been linked with an increase in obesity and type2 diabetes, i.e. a lot of bad press.
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* Sucrose
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* Xylitol
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* Vitamin C (Ascorbic Acid) from glucose
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==Sorbitol==
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'''FIXME: what is the actual pathway to make this?'''
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''E. coli'' already has sorbitol-6-phosphate dehydrogenase (srlD) which is available as <partinfo>BBa_K130000</partinfo>, which is in the distribution.
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''Borrelia burgdorferi B31'' is [http://www.ncbi.nlm.nih.gov/nuccore/15594346?from=538328&to=539275&report=gbwithparts reported to have an aldose reductase gene], as follows:
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<code style="font-size: 8pt;">
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gtgaataatcttaaagacaagataaatacttatagcaaattaattttagggtcttggcaattcggaggaggatattttaagcaagtcgaaaaagaaactg
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ctaaaaaaatattaaaaaaagcatatgatcacgggatcagaaatattgatactgcaagagcttatggaaatggaatttcggaaaaaataattggcgaaat
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aatagaaaaagatccaacaataagagaaaatattttaattgcaagtaaatgctacccaatggaaatttcagaatatagagagaactttaatgaaagtctt
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aaaaatttaaaaactgattatatagatatttactatatacactggcctaaagccgattttgacctaagaccaatcgcatcatttcttgaagaaatgagag
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taaaaggaagaataaaatatgtaggcgtaagtaattttgaaatatcacacatggaaagcataaaaaaagtttgcaaaattgacgtaaaccaaataggata
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caaccccttatttagaaataaagaaaaagatgtaattccttactgtgaagacaacaatattgccaccatatcatattcaacaattgctcaaggactttta
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tctaaagctaatataaaagacaaaaacaaatttaatgatattagaacagaaaaattgatacttttcaaaaaagaaatttggccttatactttgaaaacca
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taaataaacttgaagagatagcaaagataaataacttaacaattttagaattaacatattcatggcttaaaaaaacaaaattaagtggatttatagtggg
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ctttagcaaggaaaattatgtagaatcaaacgtaaattcatttaaagcagaaattaatgataaagtatatgaagagattacatcaattttagataatttc
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aatcaccaaacaaaaaacttcccaaatttatttaacaaaaaaatttaa</code>
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This sequence contains no forbidden sites. It does have very low GC content, though.
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This strain is available at DSMZ as [http://www.straininfo.net/strains/149324/browser DSM 4680].
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Wikipedia [http://en.wikipedia.org/wiki/Polyol_pathway claims] sorbitol cannot cross cell-membranes.
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==Fructose==
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''E. coli'' already has ''[http://www.ncbi.nlm.nih.gov/nuccore/148278?from=213&to=1535&report=gbwithparts xylA]'', the xylose isomerase gene. Still, overexpressing it may be interesting...
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<code style="font-size: 8pt;">
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atgcaagcctattttgaccagctcgatcgcgttcgttatgaaggctcaaaatcctcaaacccgttagcattccgtcactacaatcccgacgaactggtgt
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tgggtaagcgtatggaagagcacttgcgttttgccgcctgctactggcacaccttctgctggaacggggcggatatgtttggtgtgggggcgtttaatcg
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tccgtggcagcagcctggtgaggcactggcgttggcgaagcgtaaagcagatgtcgcatttgagtttttccacaagttacatgtgccattttattgcttc
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cacgatgtggatgtttcccctgagggcgcgtcgttaaaagagtacatcaataattttgcgcaaatggttgatgtcctggcaggcaagcaagaagagagcg
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gcgtgaagctgctgtggggaacggccaactgctttacaaaccctcgctacggcgcgggtgcggcgacgaacccagatcctgaagtcttcagctgggcggc
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aacgcaagttgttacagcgatggaagcaacccataaattgggcggtgaaaactatgtcctgtggggcggtcgtgaaggttacgaaacgctgttaaatacc
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gacttgcgtcaggagcgtgaacaactgggccgctttatgcagatggtggttgagcataaacataaaatcggtttccagggcacgttgcttatcgaaccga
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aaccgcaagaaccgaccaaacatcaatatgattacgatgccgcgacggtctatggcttcctgaaacagtttggtctggaaaaagagattaaactgaacat
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tgaagctaaccacgcgacgctggcaggtcactctttccatcatgaaatagccaccgccattgcgcttggcctgttcggttctgtcgacgccaaccgtggc
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gatgcgcaactgggctgggacaccgaccagttcccgaacagtgtggaagagaatgcgctggtgatgtatgaaattctcaaagcaggcggtttcaccaccg
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gtggtctgaacttcgatgccaaagtacgtcgtcaaagtactgataaatatgatctgttttacggtcatatcggcgcgatggatacgatggcactggcgct
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gaaaattgcagcgcgcatgattgaagatggcgagctggataaacgcatcgcgcagcgttattccggctggaatagcgaattgggccagcaaatcctgaaa
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ggccaaatgtcactggcagatttagccaaatatgctcaggaacatcatttgtctccggtgcatcagagtggtcgccaggaacaactggaaaatctggtaa
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accattatctgttcgacaaataa
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</code>
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This has no forbidden sites.
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==Xylitol==
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''E. coli'' has a putative xylose reductase gene, ''[http://www.ncbi.nlm.nih.gov/nuccore/48994873?from=436385&to=437359&report=gbwithparts yajO]''. It is (putatively) NADPH dependent, which I imagine means it couldn't work outside the cell...
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<code style="font-size: 8pt;">
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atgcaatacaaccccttaggaaaaaccgaccttcgcgtttcccgactttgcctcggctgtatgacctttggcgagccagatcgcggtaatcacgcatgga
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cactgccggaagaaagcagccgtcccataattaaacgtgcactggaaggcggcataaatttctttgataccgccaacagttattctgacggcagcagcga
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agagatcgtcggtcgcgcactgcgggatttcgcccgtcgtgaagacgtggtcgttgcgaccaaagtgttccatcgcgttggtgatttaccggaaggatta
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tcccgtgcgcaaattttgcgctctatcgacgacagcctgcgacgtctcggcatggattatgtcgatatcctgcaaattcatcgctgggattacaacacgc
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cgatcgaagagacgctggaagccctcaacgacgtggtaaaagccgggaaagcgcgttatatcggcgcgtcatcaatgcacgcttcgcagtttgctcaggc
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actggaactccaaaaacagcacggctgggcgcagtttgtcagtatgcaggatcactacaatctgatttatcgtgaagaagagcgcgagatgctaccactg
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tgttatcaggagggcgtggcggtaattccatggagcccgctggcaaggggccgtctgacgcgtccgtggggagaaactaccgcacgactggtgtctgatg
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aggtggggaaaaatctctataaagaaagcgatgaaaatgacgcgcagatcgcagagcggttaacaggcgtcagtgaagaactgggggcgacacgagcaca
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agttgcgctggcctggttgttgagtaaaccgggcattgccgcaccgattatcggaacttcgcgcgaagaacagcttgatgagctattgaacgcggtggat
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atcactttgaagccggaacagattgccgaactggaaacgccgtataaaccgcatcctgtcgtaggatttaaataa
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</code>
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Revision as of 13:56, 19 August 2011

Yassen will do this bit!

Retrieved from "http://2011.igem.org/Team:Edinburgh/Biorefinery"