bop (bacteriorhodopsin, P02945, Halobacterium salinarum NRC-1) - review notes

Automated deep research was UNAVAILABLE for this gene (no bop-deep-research-*.md
was generated). These notes come from my own reading of the cached PubMed records
(publications/PMID_*.md, all abstract-only), the UniProt record (bop-uniprot.txt)
and QuickGO/OLS queries made on 2026-10-15.

Gene product

• bop (VNG_1467G) encodes bacterio-opsin; with covalently bound retinal it forms
  bacteriorhodopsin (BR), the only protein of the purple membrane.
  PMID:4517939
• Precursor with a 13-residue N-terminal propeptide; mature chain 14-262 (UniProt).
  PMID:6706999
• Seven transmembrane helices; homotrimers packed into a 2D crystalline lattice (purple
  membrane) with lipids. PMID:10452895
• Retinal is bound as a protonated Schiff base on Lys216 (mature numbering; Lys229 in the
  UniProt precursor numbering). PMID:6794028

Function: light-driven outward proton pump

• Discovery of the pump: PMID:4517939
• Photophosphorylation in vivo: PMID:4524635
• Reconstitution with ATP synthase: Racker & Stoeckenius 1974 (PMID:4272126, title only in
  cache: "Reconstitution of purple membrane vesicles catalyzing light-driven proton uptake
  and adenosine triphosphate formation.").
• Mutagenesis of the proton path: PMID:3288985
• Mechanism: PMID:10949309; [PMID:10452895 "the proton acceptor Asp85"; "the proton donor Asp96"].
• Review: PMID:14977418.

Secondary role: photoreception via the proton motive force

• BR alone (in a strain lacking HR, SRI, SRII) supports phototaxis, but via Delta-mu-H+
  rather than a dedicated signalling partner. PMID:8415720
  This is the only evidence I found that rescues GO:0007602 phototransduction; the cited
  paper for that row (PMID:4517939) describes energy conversion.

Regulation (context, not annotated)

• bop is induced by low oxygen and light, under the Bat activator.
  PMID:1856168; PMID:11226271

GO landscape checks (QuickGO/OLS, 2026-10-15)

• GO:0015454 light-driven active monoatomic ion transmembrane transporter activity is a
  leaf; there is no proton-specific child (no "light-driven proton pump" term). bop
  (FlyBase, IDA, PMID:4517939) is the ONLY annotation to GO:0015454 in all of GOA.
• No archaeal protein carries GO:0016918 retinal binding or GO:0009881 photoreceptor activity.
  Bovine RHO carries GO:0005502 11-cis retinal binding by IDA, so opsins do get retinal
  binding terms.
• No GO CC term for "purple membrane" exists (searched OLS/QuickGO).
• InterPro2GO maps IPR018229 (Rhodopsin_retinal_BS) to GO:0005216 monoatomic ion channel
  activity. This hits every microbial rhodopsin I checked: halorhodopsins P0DMH7, P15647,
  P33742, sensory rhodopsin II P42196 and proteorhodopsin Q9F7P4. None of these is a
  channel (channelrhodopsins are algal). Proteorhodopsin additionally gets GO:0010461
  light-activated monoatomic ion channel activity from IPR017402.
• GO:0042777 proton motive force-driven plasma membrane ATP synthesis: experimental
  annotations are on ATP synthase subunits (plus Pyrococcus mbh subunits); the proton
  pump that generates the gradient is conventionally not annotated, so I do not propose it
  for bop.

Decisions (summary)

• REMOVE GO:0005216 channel (bR is a pump).
• ACCEPT plasma membrane (EXP, IEA) and GO:0015454 (IDA, core).
• MODIFY membrane -> plasma membrane; ion transport / ion transmembrane transport ->
  GO:1902600 proton transmembrane transport.
• KEEP_AS_NON_CORE phototransduction (secondary photoreception via PMF, PMID:8415720).
• NEW: GO:0015078 proton transmembrane transporter activity (IDA, PMID:3288985);
  GO:0016918 retinal binding (IDA, PMID:6794028).
• Proposed new terms: light-driven proton transmembrane transporter activity; purple
  membrane (CC).