rbcL (P00877, RBL_CHLRE) review notes

Process log

• 2026-10-03: Gene data were already fetched (uniprot, goa, seeded review). GOA has
  only five IEA rows (GO_REF:0000120 / GO_REF:0000104), so there are no GOA PMIDs
  to cache (fetch-gene-pmids reported none).
• Deep research: ran scripts/deep_research_wrapper.py CHLRE rbcL falcon --fallback perplexity-lite once. Falcon returned HTTP 402 Payment Required. The
  perplexity-lite fallback failed with "Provider 'perplexity' not available". I
  did not retry, and there is no deep-research file. The review is based on
  UniProt plus primary literature cached in publications/.
• Cached the following PMIDs after checking them with PubMed esummary: 11641402,
  11866526, 6302265, 9536077, 18664299, 20424165. 6302265 (Dron 1982, rbcL
  sequence) has no abstract in the cache and is not cited in the review.

Biology summary

• Chlamydomonas Rubisco is L8S8. The ~55 kDa large subunits are encoded by the
  chloroplast rbcL gene and the ~15 kDa small subunits by the nuclear rbcS family
  PMID:18664299.
• The large subunit contains the active site, and the small subunit modulates
  catalysis PMID:20424165.
• Crystal structures: 1.4 A structure with L8S8 architecture PMID:11641402. Activated enzyme with 2-CABP, where the
  large-subunit fold and active site are like spinach Rubisco PMID:11866526. PTMs: Hyp104/Hyp151 and
  S-methyl-Cys256/Cys369 PMID:11866526.
• Mg2+ cofactor, one per subunit, and Lys-201 carbamylation (UniProt, from the
  crystal structures).
• Genetics: the rbcL deletion strain MX3312 (rbcL replaced by aadA) is the host
  for chloroplast transformation with mutant rbcL genes PMID:18664299. Rubisco-null mutants are acetate-requiring
  PMID:18664299.
• Localization: quantitative immunogold shows Rubisco in both the pyrenoid and the
  stroma, about 90% in the pyrenoid at ambient CO2 and about 40% at high CO2
  PMID:9536077. Pyrenoidal Rubisco is active
  PMID:9536077.
• Pyrenoid packing is a property of the small subunit:
• Plant small subunits on algal large subunits give catalytically proficient
  Rubisco but no pyrenoid PMID:20424165.
• Two surface alpha-helices of the SSU determine pyrenoid formation
  PMID:23112177.
• EPYC1 binds the small subunit, unlike carboxysomal linkers, which bind
  between large subunits PMID:33230314. One tentative contact with large-subunit E433 is mentioned.
• Condensed Rubisco remains active PMID:30498228.

Curation decisions

• All five IEA rows are accepted: Mg2+ binding, chloroplast, carbon fixation,
  RuBP carboxylase activity, and reductive pentose-phosphate cycle.
• NEW annotations:
• GO:0009573 chloroplast Rubisco complex (IDA, crystal structures).
• GO:1990732 pyrenoid (IDA, immunolocalization, PMID:9536077).
• GO:0009570 chloroplast stroma (IDA, same paper).
• No pyrenoid assembly or condensate scaffold term is given to rbcL. The large
  subunit is part of the condensed holoenzyme but does not mediate condensation,
  which depends on the SSU helices and EPYC1.
• Photorespiration is not added. The oxygenase reaction takes place at the
  large-subunit active site, so participation is plausible. A comparator check
  against plant RBCL annotations has not been done, so this is raised as a
  question rather than asserted.

Module (pyrenoid_ccm) consistency

The rubisco_carboxylation annoton asserts complex GO:0009573, large-subunit
function GO:0016984, process GO:0019253 and location GO:1990732. The evidence
supports all four, and all four appear in core_functions. The annoton
correctly makes the small subunit, not the large subunit, the EPYC1-binding
part.