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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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New Term Request : Pipecolic Acid Biosynthesis #15634

Closed lreiser closed 6 years ago

lreiser commented 6 years ago

term: pipecolic acid biosynthesis definition: The chemical reactions and pathways resulting in the synthesis of pipecolic acid (CHEBI:17964)from L-Lysine.

is a: antimicrobial peptide biosynthetic process (GO:0002777) (maybe) is a: L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)

references: https://doi.org/10.1104/pp.17.00222 https://doi.org/10.1105/tpc.16.00486

ukemi commented 6 years ago

Hi @lreiser, I can choose the L enantiomer. Would that be more appropriate? Also not that it will be mapped to the ChEBI term for the conjugate base.

lreiser commented 6 years ago

sure. seems so. CHEBI:26142

ukemi commented 6 years ago

I have added the term without a logical def for now. Once we have the ability to import the compound from chebi, I will modify it with the correct reference.

Is it really an antimicrobial peptide? It is a single amino-acid derivative. For now I have just given it a chemical parent.

PMID:27758894 and PMID:28330936. ChEBI:30633.

ukemi commented 6 years ago

https://github.com/geneontology/go-ontology/pull/15653

lreiser commented 6 years ago

"Is it really an antimicrobial peptide? It is a single amino-acid derivative. For now I have just given it a chemical parent."

Yep you are right- bad choice there on my part

lreiser commented 6 years ago

Circling back on this from a conversation with Peifen the pipecolic acid pathway is in MetaCyc https://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-7861

So maybe include this as a cross reference. Apparently it was not in PMN bit Peifen will add it

per the last comment on the MetaCyc page "FMO1 encodes a monooxygenase that is required for both local resistance and systemic acquired resistance (SAR) [Bartsch06, Koch06, Mishina06], but the mechanism by which it regulates plant immunity is still unknown. However, it is likely that FMO1 is involved in the synthesis of a defense signal molecule that is derived from L-pipecolate [Ding16]."

The two papers referenced indicate that FMO1 is required for the conversion of L pipecolate to N-hydroxpipecolic acid which is the bioactive mobile signal.

So could we add another term? I can open this in another issue so as not to confuse things.

Term:N-hydroxypipecolic acid biosynthesis Def:The chemical reactions and pathways resulting in the synthesis of N-hydroxypipecolic acid

ukemi commented 6 years ago

I was just going to add this, but perhaps it is better to make a new request. I don't see N-hydroxypipecholate(ic acid) in ChEBI, so we will need to request it.