ybjN (P0AAY6, b0853) — curation notes

E. coli K-12 YbjN, "putative sensory transduction regulator" (Pfam PF10722 YbjN;
InterPro IPR019660; CDD cd17511 YbjN_AmyR-like). 158 aa, no catalytic motifs,
no transmembrane segment, no signal peptide in the UniProt record.

Provenance of these notes

Deep research was unavailable for this gene. No deep-research API keys are
configured in this container, so just deep-research was not run and no
-deep-research-<provider>.md file exists. Everything below comes from the
cached publications in publications/, from PubMed searches (the complete
PubMed hit list for ybjN Escherichia coli is five papers: PMID:38822378,
PMID:28426806, PMID:23028751, PMID:21980417, PMID:16701556), and from the
UniProt flat file.

The GONUTS wiki could not be consulted. https://gowiki.tamu.edu/wiki/index.php/PMID:21980417
returns only "This site is temporarily offline while we perform upgrades"
(checked 2026-10-29), matching the note in projects/CACAO.md. The four CACAO
rows were therefore judged from the paper alone — which is sufficient here,
because the single cited paper (PMID:21980417) has full text cached.

What is actually known

It is an enterobacterial orphan gene with no assigned biochemistry

YbjN orthologs are restricted to Enterobacteriaceae
PMID:21980417.
The gene sits immediately upstream of the potFGHI putrescine transport operon,
with rimK and nfsA upstream in E. coli
PMID:21980417.

The one structure of the family, Erwinia amylovora AmyR (the functionally
conserved YbjN ortholog), is a homodimer with a class I type III secretion
chaperone-like fold
PMID:28426806,
despite no secretion role; the authors read this as a protein–protein
interaction module rather than an enzyme
PMID:28426806.
Byrne et al. independently note the structural resemblance
PMID:25049088.
Note that the fold is from the Erwinia ortholog, not from E. coli YbjN
itself, so it is family-level evidence and is not used here to assert a
molecular function.

Discovery: multicopy suppressor of ts9 (coaA) temperature sensitivity

ybjN was isolated as a multicopy suppressor of the temperature-sensitive
coaA1 (pantothenate kinase L236F) allele
PMID:16701556,
and also suppresses coaA14, coaA15 and ilu-1, leading the authors to
propose a chaperone/stabilizer role
PMID:16701556.
This is an over-expression (multicopy) phenotype throughout, and no direct
holdase or stabilizer assay has been reported for YbjN.

Wang et al. confirmed the suppression and showed the ybjN transcript is
~10-fold lower in ts9 than in BW25113, and ~10-fold higher than BW when
supplied on a multicopy plasmid (Fig. 1).

Loss-of-function phenotypes (the solid, annotatable core)

All from Wang et al. 2011 (PMID:21980417), comparing BW25113 (BW), ΔybjN, and
BW carrying multicopy ybjN:

Phenotypes seen ONLY on overexpression (do not annotate)

Interaction data

The only GOA molecular-function row is a bare GO:0005515 protein binding
(IntAct IPI, PMID:24561554) with YpjF (Q46953), from the Rajagopala E. coli
binary interactome screen; the cached full text does not mention either
protein by name (the pair is in the supplementary interaction tables, and
UniProt records it as P0AAY6; Q46953: ypjF; NbExp=3). Suggestive, given that
multicopy ybjN induces toxin–antitoxin modules and YpjF is a YpjF/YfjZ-type
toxin, but a Y2H pair is not a molecular function. Removed under the
protein-binding policy (removal does not dispute the interaction).

Reading for the CACAO audit

Four of the seven GOA rows are CACAO, all IMP from PMID:21980417, all on the
right gene and the right paper with an evidence code that fits the assay. Two
are right (biofilm, flagellum assembly). Two fail: