lmse/fyrment

Fungi pan-genome-scale network reconstruction

fyrment's Issues

Add polyol phosphatase, important for glycolysis kinetics

Discovery and functional characterization of a yeast sugar alcohol phosphatase.

"Sugar alcohols (polyols) exist widely in nature. While some specific sugar alcohol phosphatases are known, there is no known phosphatase for some important sugar alcohols (e.g., sorbitol-6-phosphate). Using liquid chromatography-mass spectrometry-based metabolomics, we screened yeast strains with putative phosphatases of unknown function deleted. We show that the yeast gene YNL010W, which has close homologues in all fungi species and some plants, encodes a sugar alcohol phosphatase. We term this enzyme, which hydrolyzes sorbitol-6-phosphate, ribitol-5-phosphate, and (D)-glycerol-3-phosphate, polyol phosphatase 1 or PYP1. Polyol phosphates are structural analogs of the enediol intermediate of phosphoglucose isomerase (Pgi). We find that sorbitol-6-phosphate and ribitol-5-phosphate inhibit Pgi and that Pyp1 activity is important for yeast to maintain Pgi activity in the presence of environmental sugar alcohols. Pyp1 expression is strongly positively correlated with yeast growth rate, presumably because faster growth requires greater glycolytic and accordingly Pgi flux. Thus, yeast express the previously uncharacterized enzyme Pyp1 to prevent inhibition of glycolysis by sugar alcohol phosphates. Pyp1 may be useful for engineering sugar alcohol production."

https://www.ncbi.nlm.nih.gov/pubmed/30240188

Riboneogenesis in yeast

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163394/

add metabolites from riboneogensis paper

s1p
o1p
o8p
s17bp (already present)
o18bp

to yeast pan-genome model

Review SO dimutase in rgm which is currently missing

rgm
SPODM
2 o2s[c] + 2 h[c] -> h2o2[c] + o2[c]

The Sub‐Cellular Localisation of Pyruvate Carboxylase and of Some Other Enzymes in Aspergillus nidulans

Add to pan-GENRE with FOG annotation

https://febs.onlinelibrary.wiley.com/doi/abs/10.1111/j.1432-1033.1983.tb07499.x

Add Pho13p promiscuous enzyme activity

a conserved phosphatase destroys toxic glycolytic side products in mammals and yeast

Enzymatic Production of Glyoxal from Ethylene Glycol Using Alcohol Oxidase from Methanol Yeast

Review enzyme activities assigned to alcohol oxidase

https://www.tandfonline.com/doi/abs/10.1271/bbb.58.170

Reconcile differences with iJB1325 for Aspergillus

https://link.springer.com/article/10.1186/s40694-018-0060-7

Identification and characterization of two fatty acid elongases in Lipomyces starkeyi

https://link.springer.com/article/10.1007%2Fs00253-020-10401-9

Degradation of 1,4-Dioxane and Cyclic Ethers by an Isolated Fungus

https://aem.asm.org/content/71/3/1254.short

"By using 1,4-dioxane as the sole source of carbon, a 1,4-dioxane-degrading microorganism was isolated from soil. The fungus, termed strain A, was able to utilize 1,4-dioxane and many kinds of cyclic ethers as the sole source of carbon and was identified as Cordyceps sinensis from its 18S rRNA gene sequence. Ethylene glycol was identified as a degradation product of 1,4-dioxane by the use of deuterated 1,4-dioxane-d8 and gas chromatography-mass spectrometry analysis. A degradation pathway involving ethylene glycol, glycolic acid, and oxalic acid was proposed, followed by incorporation of the glycolic acid and/or oxalic acid via glyoxylic acid into the tricarboxylic acid cycle."

Models should have mitochondrial DNA/RNA/protein biosynthesis

Biomass equation is currently based on [c] only.