Rules for Classification of terpene pathway - petermr/CEVOpen GitHub Wiki

With this we confirm that we have a Terpene Pathway.

  1. Only If the following figure is a pathway, can it be a metabolic pathway.
  2. Only If the following figure is a metabolic pathway, can it be a terpene biosynthetic pathway.
  3. If any part of the image contains our target pathway we say yes to that entry.

Please fill each of these columns with "yes" and "no".

PMCID Fig No. Pathway Metabolic Pre-Terpene Terpene Terpene Synthase
           

Rules for identifying Pathway:

  1. Any series of event leading to a product or depiction of chain of events
  2. Breakdown of a substrate into various sub products or transfer of metabolites or genetic transformation under a closed boundary of a cell wall or inside a cytoplasm.
  3. Multiple arrows or interconversions between elements can be our indicator.

Rules for identifying Metabolic Pathway:

  1. See if it has biochemical molecules for example as shown in fig, they are generally, carbohydrates, lipids, nucleic acids, and proteins:
  2. In general a metabolic pathway are linked series of biochemical reactions
  3. Key Point: Metabolites that comprises reactant, product and intermediates product of enzymatic reactions.
  4. Could also see there would be catalysts: enzymes, co-factors etc.
  5. If the pathway ends with a molecule not a process then it's a metabolic pathway.

Examples of metabolic pathway:

Rules for identifying Pre-Terpene Pathway:

  1. First, look for anything ending with terpene, Basic unit of terpene is isoprene:
  2. Terpenes are derived from alkenes so often the compounds ending with “ene” for eq: limonene, myrcene
  3. All terpenes are derived from a small number of starting point (isoprenoids) with multiple double bonds.
  4. Many diagrams give an explicit pathway (MVA/MEP) which creates starting terpenes mentioned below, if they are present as the end product than it's a pre-terpene pathway representation.
    • farnesene
    • farnesyl pyrophosphate (FPP)
    • Geranyl Diphosphate (GPP)
    • Geranylgeranyl diphosphate (GGPP)
    • Squalene
    • Phytoene
  5. They often have added oxygen (eg: alcohols, ketones, acids, asters). For eg: terpineol, retinol, hinokitiol.
  6. Then, see if somewhere IPP —> DMAPP, this kind of conversion is occurring. (identifying)
    • https://en.wikipedia.org/wiki/Isopentenyl-diphosphate_delta_isomerase Now if these elements are present, we just have to spot if there’s a mevalonate or mep pathway, as we could produce terpene only by these two pathway:
      • For MVA Pathway, there’s mevalonic acid present (key point), here acetyl Co-A (key point) is being converted through series of enzymatic reaction into IPP —> DMAPP or
      • For MEP Pathway, there’s methylerythritol 4-phosphate present (key point), here Pyruvate + glyceraldehyde 3 phosphate (key point) is being converted through series of enzymatic reaction into IPP —> DMAPP

Example of Pre-Terpene Pathway:

Rules for identifying Terpene Pathway:

  1. It’s a continuum to the pre terpene pathway; a figure could have a diagrammatic representation of terpene conversion without mev/mva listed there; those are listed as terpene pathways.
  2. The ending of the pathway should have unique terpenes, should not be ending with farnesene, farnesyl pyrophosphate (FPP), Geranyl Diphosphate (GPP), Geranylgeranyl diphosphate (GGPP), Squalene.
  3. If the pathway is not ending with farnesene, farnesyl pyrophosphate (FPP), Geranyl Diphosphate (GPP), Geranylgeranyl diphosphate (GGPP), Squalene but they are an intermediate prodocut then if they have any three of the following points then mark it as Terpene Pathway:
    • If there's downstream conversions happening after these starting terpene
    • If the following pathway is ending with any named compound
    • If there's any Terpene Synthase Enzyme catalyzing the reaction
  4. Also if any common derivatives of terpene i.e. Monoterpenes, Diaterpenes, Sesquiterpenes, Sesterpenes, Triterpenes, Tetraterpenes and Polyterpenes are present as end product don’t mark it as a terpene pathway.
  5. Some common terpene inputs that may be an indicator like: TPS (Terpene Synthase) which enzyme (catalyst) is responsible for ring formation or addition of a functional group (-OH, =O, acid etc.) to a biosynthetic molecule.
  6. If there’s conversions happening and leading to formation of terpene we could definitely say it’s a terpene pathway.
  7. After going through all this rules only one can state that it’s a terpene biosynthetic pathway

Examples of Terpene Pathway:

Rules for identifying Terpene Synthase:

  1. There are some catalytic enzymes that are resonsible for formation of unique terpnes.
  2. They are generally found after the isoprenoids i.e. starting terpenes and catalyzes the reaction by converting the starting terpene into unique terpenes.
  3. Mostly are written in short form as a catalyst: TPS, GGPS, FDPS, SPS.

Examples of Terpene Synthase:

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