arnE manual review notes

Deep research and FEBA fitness output were not available for this arnE pass.
These notes are grounded in the local UniProt record for Q47377, the paired
arnF review, and the cached publications cited by the seeded arnE GOA rows.

Identity

• UniProt: Q47377, ARNE_ECOLI
• Preferred gene symbol: arnE
• Older names: pmrL, yfbW
• Ordered locus names: b4544, JW2252
• Product: probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase
  subunit ArnE
• Protein: 111 aa, inner-membrane multi-pass protein with an EamA domain
• Family context: ArnE-family member in the DMT/SMR transporter superfamily

Core function

ArnE/PmrL is one of the two small inner-membrane proteins required to flip
undecaprenyl phosphate-alpha-L-Ara4N from the cytoplasmic to periplasmic face of
the inner membrane. Yan, Guan, and Raetz directly analyzed E. coli pmrL/arnE and
pmrM/arnF deletion mutants and concluded that "PmrL and PmrM could specifically
function to flip undecaprenyl phosphate-alpha-L-Ara4N from the cytosolic to the
periplasmic side of the inner membrane, possibly functioning as a heterodimer"
PMID:17928292.

The lipid-linked L-Ara4N donor is synthesized on the cytoplasmic face and has to
reach the periplasmic face before ArnT can transfer L-Ara4N to lipid A. In the
pmrL or pmrM mutants, more than 95% of L-Ara4N-modified lipid A was missing
PMID:17928292, but the donor pool itself was not
depleted PMID:17928292. The decisive
labeling experiment used membrane-impermeable sulfo-NHS-biotin and found a
4-5-fold reduction in periplasmically accessible donor in the arnE/arnF mutants
PMID:17928292.

Annotation decisions

• GO:0005886 plasma membrane is accepted for all IDA/IBA/IEA rows because this
  is the GO component for the E. coli inner membrane. Daley et al. mapped 601
  E. coli inner-membrane proteins by C-terminal PhoA/GFP tagging PMID:15919996.
• GO:0022857 transmembrane transporter activity is too generic for the exact
  activity. ArnE/ArnF flips a lipid-linked donor between leaflets of the same
  membrane, so the best existing molecular-function term is GO:0140303 intramembrane lipid transporter activity, matching the already reviewed ArnF
  partner.
• The three GO:1901505 carbohydrate derivative transmembrane transporter activity rows are retained. They are less exact about lipid flipping than
  GO:0140303, but undecaprenyl phosphate-alpha-L-Ara4N carries a carbohydrate
  derivative and the term is not merely a generic SMR transporter mapping.
• GO:1901264 carbohydrate derivative transport, GO:0046493 lipid A metabolic process, GO:1901760 beta-L-Ara4N-lipid A biosynthetic process,
  GO:0009245 lipid A biosynthetic process, and GO:0009103 lipopolysaccharide biosynthetic process are all accepted because ArnE does the
  flippase step that places the donor for L-Ara4N modification of lipid A.
• The two GO:0010041 response to iron(III) ion rows are real regulatory
  observations but over-annotate arnE's protein function. Hagiwara et al. showed
  the yfbE/arn operon is induced by external iron in a BasS-BasR-dependent manner
  PMID:15322361; arnE itself is a lipid
  donor flippase subunit, not an Fe(III) sensor or detoxification protein.

Ontology note

GO:0140303 intramembrane lipid transporter activity is the conservative exact
existing term for ArnE. GO has more specific ATP-coupled flippase/floppase
children and a non-selective scramblase branch, but no specific child for an
ATP-independent, directional, substrate-specific transporter of an undecaprenyl
phosphate-linked sugar. The arnF review makes the same call for the same
two-subunit system.