reworking all metabolic phenotypes

[dsiegele]

2013-05-22 Jonathan Herrera: -metabolic phenotype ----------biosynthetic phenotype (move aux from its sibling term to child term) ----------------Small Molecule ----------------prototrophic ----------------auxotrophic ----------------AA biosynthesis -------------------------------ability to synthesize AA, state phenotype -------------------------------inability to synthesize AA, state phenotype --------------------------------Ability to synthesize AA, relative phenotype ----------------------------------------------------Decrease Amino Acid Biosynthesis ----------------------------------------------------increase Amino Acid Biosynthesis -----------------------{All 20 AA) biosynthesis ------------------------------ability to synthesize Methionine, State Phenotype ------------------------------Inability to synthesize Methionine, state phenotype ------------------------------Ability to synthesize, relative phenotype ----------------------------------------------------Decrease methionine biosynthesis, Relative ----------------------------------------------------Increase Methionine biosynthesis, relative -----------------------Etc. ----------------vitamin biosynthesis ---------------------------------ability to synthesize vitamin, state phenotype ---------------------------------Inability to synthesize Vitamin, state phenotype ---------------------------------Ability to synthesize vitamin, relative Phenotype ----------------------------------------------------decrease synthesis of vitamin, relative ----------------------------------------------------increase synthesis of Vitamin, relative ---------------------------(all Vitamin) Biosynthesis ---------------------------------Ability to synthesize Vit K2, State Phenotype (K1 cannot be synth by e. coli) ---------------------------------Inability to synthesize Vit K2, State Phenotype ---------------------------------Ability to synthesize Vitamin, Relative phenotype ----------------------------------------------------Decrease Synthesis of vit K2, relative ----------------------------------------------------Increase Synthesis of fit K2, relative ----------------------Etc. ----------------purine biosynthesis ----------------------------------ability to synthesize purine, state phenotype ----------------------------------inability to synthesize purine, state phenotype ----------------------------------ability to synthesize purine, relative phenotype ----------------------------------------------------increase synthesis of purine, relative ----------------------------------------------------decrease synthesis of purine, relative --------------------------adenine biosynthesis ---------------------------------ability to synthesize adenine, state phenotype ---------------------------------inability to synthesize adenine, state phenotype ---------------------------------ability to synthesize adenine, relative phenotype ---------------------------------------------------increase synthesis of adenine, relative ---------------------------------------------------decrease synthesis of adenine, relative --------------------------guanine biosynthesis ---------------------------------ability to synthesize guanine, state phenotype ---------------------------------inability to synthesize guanine, state phenotype ---------------------------------ability to synthesize guanine, relative phenotype ---------------------------------------------------increase synthesis to guanine, relative ---------------------------------------------------decrease synthesis to guanine, relative ----------------pyrimidine biosynthesis ---------------------------------ability to synthesize pyrimidine, state phenotype ---------------------------------inability to synthesize pyrimidine, state phenotype ---------------------------------ability to synthesize pyrimidine, relative ---------------------------------------------------increase synthesis of pyrimidine, relative ---------------------------------------------------decrease synthesis of pyrimidine, relative ------------------------cytosine biosynthesis ---------------------------------ability to synthesize cytosine, state phenotype ---------------------------------inability to synthesize cytosine, state phenotype ---------------------------------ability to synthesize cytosine, relative ---------------------------------------------------increase synthesis to cytosine, relative ---------------------------------------------------decrease synthesis to cytosine, relative ------------------------thymine biosynthesis ---------------------------------ability to synthesize thymine, state phenotype ---------------------------------inability to synthesize thymine, state phenotype ---------------------------------ability to synthesize thymine, relative phenotype ---------------------------------------------------increase synthesis of thymine, relative ---------------------------------------------------decrease synthesis of thymine, relative ------------------------uracil biosynthesis ---------------------------------ability to synthesize uracil, state phenotype ---------------------------------inability to synthesize uracil, state phenotype ---------------------------------ability to synthesize uracil, relative phenotype ---------------------------------------------------increase synthesis of thymine, relative ---------------------------------------------------decrease synthesis of thymine, relative ----------------lipid biosynthesis ---------------------------------ability to synthesize lipids, state phenotype ---------------------------------inability to synthesize lipids, state phenotype ---------------------------------ability to synthesize lipids, relative phenotype ---------------------------------------------------increase synthesis of lipids, relative ---------------------------------------------------decrease synthesis of lipids, relative -----------------------Fatty Acid biosynthesis ---------------------------------ability to synthesize fatty acids, state phenotype ---------------------------------inability to synthesize fatty acids, state phenotype ---------------------------------ability to synthesize fatty acids, relative ---------------------------------------------------increase synthesis of fatty acids, relative ---------------------------------------------------decrease synthesis of fatty acids, relative For Lipids we can add as we come across annotations. Some light reading on wikipedia shows that we might end up having 8 lipid child terms. "fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits)." http://en.wikipedia.org/wiki/Lipids#cite_ref-Raetz2006_42-1

[dsiegele]

2013-05-22 Jonathan Herrera: Definition of LIPID is from the same paper setting up the 8 group classification system: "For the purpose of classification, we define lipids as hydrophobic or amphipathic small molecules that may originate entirely or in part by carbanion-based condensations of thioesters (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides) and/or by carbocation-based condensations of isoprene units (prenol lipids and sterol lipids)." PMID: 19098281

[dsiegele]

2013-05-22 Jim Hu: Should these be biosynthesis or growth in the absence of exogenous nutrient X?

[dsiegele]

2013-05-22 Jonathan Herrera: If I understand your questions I believe it's biosynthesis. Aux exists, as a sibling term (to biosynthesis of all listed) for the purpose of having a term for papers that do not bother to figure out what specific AA, or any other small molecule, missing causes a stop growth.

[dsiegele]

2013-05-24 Jonathan Herrera: Clarification on structure. Small molecule is not a sibling term to prototrophic, aux, AA synthesis, etc. It should be a parental term to all those, but a child term to biosynthetic phenotype. See: -metabolic phenotype ------------biosynthetic phenotype (move aux from its sibling term to child term) -------------------Small Molecule --------------------------prototrophic (it can make all organic molecules it needs) --------------------------auxotrophic --------------------------AA biosynthesis ------------------------------etc Although, I still have issues with how we are have terms small molecule vs macromolecule. Do we mean monomer in place of small molecule? small molecule was there before I reworked these nodes so I am unclear on the original definition. It also seems that it might not fit with what we have since some sources claim lipids as macromolecules.

[dsiegele]

2013-07-12 Jonathan Herrera: Need to put a hold on this for now, do not release. Debby and Jim discussed reorganizing everything under Nutrient utilization, will be discussed at next meeting.

[dsiegele]

2015-03-13 This group of terms was requested while we were still working out how to organize the biosynthesis branch. For amino acids and vitamins (growth factors) we decided to not have terms for individual compounds, but to indicate the particular compound that is affected in the 'column 16' equivalent.