Aromatic Amino Acid Biosynthetic Process, Prephenate Pathway — Obsoletion

IN_PROGRESS OBSOLETION

Aromatic Amino Acid Biosynthetic Process, Prephenate Pathway — Obsoletion

Overview

A GO obsoletion proposal will obsolete GO:0009095 aromatic amino acid family biosynthetic process, prephenate pathway. The term is a pre-composed
representation of two distinct downstream pathways (L-phenylalanine biosynthesis
and L-tyrosine biosynthesis) and corresponds to the combined MetaCyc
superpathway PWY-3481 superpathway of L-phenylalanine and L-tyrosine biosynthesis. The two component pathways are already represented separately as
GO:0009094 L-phenylalanine biosynthetic process (xref MetaCyc:PWY-3462) and
GO:0006571 L-tyrosine biosynthetic process (xref MetaCyc:PWY-3461), so the
combined parent term is redundant.

The four experimental annotations on the upstream list are spread across three
genes/proteins in three organisms (Arabidopsis, Petunia, Mycobacterium
tuberculosis). The upstream issue was opened by Raymond Lee (WormBase), who
inspected each publication and proposed concrete actions — for the most part,
removal rather than relabeling, because none of the cited papers actually
establish a BP role in either component pathway. The annotation review ticket
itself (geneontology/go-annotation#6395) is assigned to Antonia Lock for
coordination of the per-group cleanup.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Suggested replacements
aromatic amino acid family biosynthetic process, prephenate pathway GO:0009095 GO:0009094 L-phenylalanine biosynthetic process and/or GO:0006571 L-tyrosine biosynthetic process

Term labels and live status verified in OLS on 2026-05-14:
- GO:0009095 — aromatic amino acid family biosynthetic process, prephenate pathway (still live; obsoletion proposed but not yet applied)
- GO:0009094 — L-phenylalanine biosynthetic process (live)
- GO:0006571 — L-tyrosine biosynthetic process (live)

The replacements are downstream subprocesses, not synonyms — moving an
annotation to a replacement is only valid if the supporting paper actually
establishes a role in phenylalanine or tyrosine biosynthesis specifically. The
reviewer's analysis suggests that for three of the four annotations, the
underlying papers do not support either replacement and the cleanest action
is removal.

Affected experimental annotations (upstream list)

# Source Accession Symbol Taxon PMID Evidence Reviewer's proposed action
1 UniProt UniProtKB:Q9SIE1 PAT NCBITaxon:3702 (Arabidopsis thaliana) PMID:21102469 EXP Remove — paper does not show a BP role for Arabidopsis PAT
2 UniProt UniProtKB:E9L7A5 PPA-AT NCBITaxon:4102 (Petunia hybrida) PMID:21102469 EXP Reannotate to GO:0009094 L-phenylalanine biosynthetic process — Fig 1 shows PPA-AT RNAi affects L-Phe biosynthesis
3 TAIR UniProtKB:Q9SIE1 (AGI: AT2G22250; Arabidopsis PAT) PAT NCBITaxon:3702 PMID:20883697 EXP Remove — biochemical paper, no BP information
4 MTBBASE UniProtKB:P9WIC1 Rv0948c (intracellular chorismate mutase) NCBITaxon:83332 (Mycobacterium tuberculosis H37Rv) PMID:18727669 EXP Remove — biochemical/structural paper, no BP information

Group impact tally (from upstream): UniProt 2, TAIR 1, MTBBASE 1.

UniProt protein names verified via UniProtKB REST on 2026-05-14:
- Q9SIE1 (Arabidopsis PAT): "Bifunctional aspartate aminotransferase and
glutamate/aspartate-prephenate aminotransferase"
- E9L7A5 (Petunia PPA-AT): "Bifunctional aspartate aminotransferase and
glutamate/aspartate-prephenate aminotransferase"
- P9WIC1 (M. tuberculosis Rv0948c): "Intracellular chorismate mutase"

Mappings flagged for redirection

None. The upstream issue states there are no InterPro2GO, UniProt-Keywords, or
UniRule mappings to GO:0009095 (only the MetaCyc:PWY-3481 xref on the term
itself). The obsoletion is therefore a pure annotation/ontology cleanup with no
mapping fan-out.

Impact on this repo

None of the three affected genes currently have an *-ai-review.yaml in this
repo (verified on 2026-05-14 via find genes -iname '*PAT*' -path '*ARATH*',
find genes -iname '*PPA*', and find genes -iname '*Rv0948*'). There is also
no existing project covering aromatic amino acid biosynthesis or chorismate
metabolism. This project is therefore a queueing exercise; no live reviews need
to be updated.

Scope

Candidate genes for initial review

Listed in priority order. Each should be set up with
just fetch-gene <organism> <gene> before review begins.

  1. PPA-AT (Petunia hybrida, E9L7A5) — Highest-value review on this list:
    the upstream proposal is to reannotate (not remove) this entry to
    GO:0009094 L-phenylalanine biosynthetic process based on Fig 1 RNAi
    evidence in PMID:21102469. The AI review should confirm the figure
    actually supports L-phenylalanine specifically (vs. tyrosine or both) and
    record the reannotation as MODIFY with the proposed replacement term.
  2. PAT (Arabidopsis thaliana, Q9SIE1) — Carries two of the four affected
    annotations (PMID:21102469 + PMID:20883697). Both proposed actions are
    removal. Review should confirm that neither paper establishes a BP role and
    record REMOVE for each entry. PMID:20883697 in particular is a pure
    biochemical characterisation, so the BP annotation is best characterised as
    over-annotation.
  3. Rv0948c (Mycobacterium tuberculosis, P9WIC1) — Intracellular chorismate
    mutase. PMID:18727669 is a biochemical/structural paper. Proposed action is
    removal. This is also a useful test case for cross-organism aromatic
    amino acid biosynthesis annotation patterns; chorismate mutase activity
    itself sits upstream of both phenylalanine and tyrosine biosynthesis but is
    not specific to either, so even a remap to GO:0009094 or GO:0006571
    would not be defensible without in-vivo data.

Proposed approach

  1. Wait for the obsoletion to land before bulk action. GO ontology ticket
    #32005 is closed (Steven Marygold proposed it) but the annotation review
    ticket #6395 is still open with reviewer assigned (Antonia Lock). Per-gene
    AI reviews can proceed independently — the action codes (REMOVE vs MODIFY)
    are what matter and are stable regardless of obsoletion timing.
  2. Start with Petunia PPA-AT. It is the only annotation on the list with a
    proposed positive replacement (MODIFY → GO:0009094). The PMID:21102469
    Fig 1 RNAi check is concrete and fast.
  3. Do the two Arabidopsis PAT annotations together. Same gene, same
    organism — the two reviews share the gene-fetch and notes work, and the
    evidence base for both is biochemical-only. Likely outcome: REMOVE on both.
  4. M. tuberculosis Rv0948c last. Mycobacterium chorismate mutase is a
    smaller scientific lift but is also the most clearly correct REMOVE on
    the list (biochemical/structural paper, no BP claim), so it is the
    lowest-priority confirmation review.
  5. No upstream mapping fan-out. Unlike obsoletions that involve InterPro2GO
    or UniRule mappings, GO:0009095 has no such mappings — there is no
    additional flag-to-upstream task here.

Priority

Low–Medium. The biology is mostly settled (the reviewer has already done the
hard work), and the affected gene set is small (3 genes, 4 annotations). The
Petunia PPA-AT review is the most interesting case because it converts a
generic prephenate-pathway annotation into a substrate-specific
phenylalanine-biosynthesis annotation; the rest are cleanup.

Status