Microorganisms engineered to use unconventional sources of phosphorous or sulfur
Disclosed are genetically engineered organisms, such as yeast and bacteria, that have the ability to metabolize atypical phosphorus or sulfur sources. Fermentation methods using the genetically engineered organisms are also described. The fermentation methods are robust processes for the industrial bioproduction of a variety of compounds, including commodities, fine chemicals, an pharmaceuticals.
1. A method for converting a substrate to a product, the method comprising the step of
contacting a genetically engineered yeast microorganism with the substrate to produce the product,
wherein
the genetically engineered yeast microorganism is a species of the genus Yarrowia, Saccharomyces or Arxula;
the genetically engineered yeast microorganism has been transformed by a nucleic acid molecule; the nucleic acid molecule comprises a non-native gene, the non-native gene is not found within a native yeast microorganism of the same species as the genetically engineered yeast microorganism; and the non-native gene encodes for a non-native enzyme comprising NAD:phosphite oxidoreductase (phosphite dehydrogenase); and
the substrate comprises a phosphorus-containing compound of any one of Formulas I-III; wherein
the compound of formula I is
wherein, independently for each occurrence,
R is —H, —OH, alkyl, —OR 2 , —SH, or —SR 2 ;
R 1 is —H, or alkyl;
Y is O or S;
Y 1 is O or S; and
R 2 is alkyl;
the compound of formula II is
wherein, independently for each occurrence,
R 1 is —H, or alkyl; and
Y 1 is O or S; and
the compound of formula III is
wherein, independently for each occurrence,
R 3 is —H, —OH, —OR 4 , —SH, —SR 4 , halo, alkyl, aryl, heteroaryl, aralkyl, or heteroaralkyl; and
R 4 is alkyl or aryl.
2. The method of claim 1 , wherein the phosphorus-containing compound is selected from the group consisting of:
3. The method of claim 1 or 2 , wherein the product is ethanol, isopropanol, lactic acid, an isoprenoid, a lipid, butanol, 1,3-propanediol, 1,4-butanediol, succinic acid, an expressed protein product, a polyol, or itaconic acid.
4. The method of claim 1 , wherein the non-native gene comprises ptxD.
5. The method of claim 1 , wherein the non-native gene comprises Pseudomonas stutzeri WM88 ptxD.
6. The method of claim 1 , wherein the genetically engineered yeast microorganism is selected from the group consisting of Yarrowia lipolytica, Saccharomyces cerevisiae , and Arxula adeninivorans.
7. The method of claim 1 , wherein the nucleic acid molecule comprises SEQ ID NO:11.
8. The method of claim 1 , wherein the NAD:phosphite oxidoreductase comprises SEQ ID NO:10.
9. The method of claim 1 , wherein the phosphorus-containing compound is a compound of Formula I.
10. The method of claim 1 , wherein the genetically engineered yeast microorganism sequesters the product.
11. The method of claim 1 , wherein the substrate does not comprise an antibiotic.
12. The method of claim 1 , wherein the substrate further comprises a lignocellulosic material, glucose, xylose, sucrose, acetic acid, formic acid, lactic acid, butyric acid, a free fatty acid, dextrose, glycerol, fructose, lactose, galactose, mannose, rhamnose, or arabinose, or a combination thereof.
13. The method of claim 1 , wherein the pH of the substrate is from about 2.5 to about 10.
14. The method of claim 1 , wherein the genetically engineered yeast microorganism is contacted with the substrate at a temperature of from about 15° C. to about 80° C.
15. The method of claim 1 , wherein the genetically engineered yeast microorganism is contacted with the substrate over a time period of from about 6 hours to about 10 days.
16. The method of claim 1 , wherein the genetically engineered yeast microorganism is contacted with the substrate in a fermenter.
17. The method of claim 1 , wherein the genetically engineered yeast microorganism is contacted with the substrate in an industrial-size fermenter.
18. The method of claim 1 , wherein the substrate comprises the phosphorus-containing compound in about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100% by weight.
19. The method of claim 3 , wherein the expressed protein product is an enzyme product.
20. The method of claim 1 , wherein the substrate comprises the phosphorus-containing compound in an amount from about 10% by weight to about 100% by weight.