LCIB (Chlamydomonas reinhardtii, UniProt Q75NZ2) - curation notes

Provenance of this review

• 2026-10-03: GOA file for Q75NZ2 is empty (header only). There are no existing
  GO annotations to review; all entries in existing_annotations are NEW.
• Deep research was not run. The falcon provider currently returns HTTP 402
  and perplexity is unavailable, so no -deep-research-*.md file exists. The
  literature below was found by PubMed esearch ("LCIB AND Chlamydomonas",
  "pmp1 AND Chlamydomonas", "ad1 AND air-dier") and cached with
  ai-gene-review fetch-pmid.
• Jin et al. 2016 (PMID:27911826) is abstract-only in the cache. I read the full
  text at PMC5187666 to check which LCIB homologs had CA activity (see below).
  Those full-text statements cannot be quoted as supporting_text because the
  cached file has only the abstract; they are described in review text instead.

Identity

• UniProt Q75NZ2 (TrEMBL, 448 aa, gene name LciB), Pfam PF18599 LCIB_C_CA,
  InterPro IPR040703 (LCIB/C_CA), PANTHER PTHR38016:SF1.
• LCIB is the gene mutated in the classical air-dier mutants pmp1 and ad1
  PMID:16777959
• Air-dier phenotype: dies at air CO2 but grows at high and very low CO2
  PMID:16777959
• Small family of four related soluble plastid proteins (LCIB, LCIC, LCID, LCIE)
  PMID:16777959
• Strongly induced at low CO2 under CCM1 control (PMID:15235119, the paper that
  deposited the AB168093 cDNA).

Complex with LCIC

• PMID:20660228
• PMID:20660228
• Loss of LCIB destabilises LCIC: PMID:34791500
• Jin et al. (full text, PMC5187666) found that co-expressed recombinant LCIB and
  LCIC form a ~440 kDa complex at 1:1 stoichiometry, whereas mixing separately
  purified proteins did not reconstitute it; LCIB alone forms a ~390 kDa
  homo-oligomer and LCIC alone a dimer.
• LCIB, LCIC and EPYC1 co-occur in the Mackinder spatial interactome
  PMID:28938113

Localization

• Chloroplast stroma, soluble; under very low CO2 it relocates to a ring around
  the pyrenoid, outside the starch sheath.
  PMID:34791500
  PMID:34791500
• Relocation requires LCIC and is switched at ~7 uM CO2
  PMID:34791500
• Light and low-CO2 dependent; diffuses away in the dark or at high CO2
  PMID:20660228
  Note that Yamano et al. 2022 later found that relocation at very low CO2 can
  happen in the dark (PMID:34791500 abstract), so the light requirement depends
  on CO2 level.
• Starch sheath is required for peripheral localization
  PMID:32041908
  and LCIB itself has no starch-binding domain
  PMID:32041908
• Mislocalisation mutants (abl) have CCM defects
  PMID:24384670
• Decision: location = GO:0009570 chloroplast stroma. I do NOT use GO:1990732
  pyrenoid: LCIB sits outside the starch sheath around the matrix, not in the
  Rubisco matrix.

Molecular function: carbonic anhydrase (beta-CA fold) - with caveats

• Structure: Jin et al. 2016 solved CrLCIB and CrLCIC structures with
  beta-CA-like zinc sites
  PMID:27911826
  PMID:27911826
• Careful: the three CA-active homologs were NOT the Chlamydomonas proteins.
  Full text (PMC5187666): "PtLCIB3, PtLCIB4, and FjLCIB exhibited diverse levels
  of CA activity ... whereas CsLCIB, CrLCIB, CrLCIC, recombinant CrLCIB-LCIC
  complex, and native CrLCIB-LCIC complex were inactive under all conditions
  tested". The zinc site (Cys120, His180, Cys204 in CrLCIB) is present, but the
  loop carrying the catalytic His162/Arg194 equivalents is disordered, and an
  Arg at the position of PtLCIB4 Ser47 (Arg121) restricts dimer gap closure;
  back-mutation R121S did not restore activity. The authors proposed a tightly
  regulated CA in Chlamydomonas.
• Heterologous complementation (Kasili et al. 2023):
  PMID:36856938
  PMID:36856938
  PMID:36856938
  Abstract-only in cache. This is a genetic (complementation) argument, IGI.
• Tobacco stromal expression raises total leaf CA activity (Barsoum et al. 2026)
  PMID:42328090
  PMID:42328090
  Caveat: a crude-extract measurement; could include indirect effects on
  endogenous CAs, but consistent with intrinsic activity.
• Wang & Spalding review (2014) predates the structure and calls LCIB motif-less
  PMID:24307449
• Decision: GO:0004089 carbonate dehydratase activity is supported for LCIB by
  two independent heterologous gain-of-function assays (yeast, Arabidopsis)
  plus increased CA activity in tobacco, and by a beta-CA zinc site in the
  crystal structure. Direct in-vitro CA activity of purified CrLCIB or of the
  native LCIB-LCIC complex has NOT been shown (Jin 2016 negative). I assert it
  as molecular_function (LCIB alone complements, so it is not only a
  contributes_to relationship) but flag the in vitro discrepancy in the review
  and in suggested experiments.

Physiological role: CO2 recapture / CO2 uptake into stromal Ci pool

• Genetic placement downstream of CAH3
  PMID:19074623
• Suppressor screen
  PMID:21409559
• Distinct from LCIA bicarbonate uptake
  PMID:25336519
• HLA3 knockdown in lcib background
  PMID:19321421
• Modelling (Fei et al. 2022) treats LCIB/LCIC as the stromal CA that converts
  CO2 to bicarbonate, and its pyrenoid-peripheral relocation as reducing leakage
  PMID:35596080

GO biological process

• GO has no "CO2-concentrating mechanism" process term (searched "carbon
  concentrat", "carbon dioxide"; only transport/response/detection terms).
  I do not propose a NEW BP. "response to carbon dioxide" would describe the
  induction of LCIB expression rather than LCIB's work. Raised as a question.

Complex

• No GO cellular component term for the LCIB-LCIC complex. Proposed as a new
  term; in_complex left unset because the field requires a GO complex id.

Module assertion check (modules/pyrenoid_ccm.yaml, annoton lcib_lcic_ca)

• carbonate dehydratase activity GO:0004089: supported (complementation,
  structure), with the caveat that purified Chlamydomonas protein/complex was
  inactive in vitro (Jin 2016). The module text "CA activity of the
  Chlamydomonas complex itself has not been robustly measured in vitro" is
  accurate. The evidence statement for PMID:27911826 ("several LCIB-family
  homologs are functional CAs") is also accurate, but readers should know that
  the CA-active homologs were diatom/bacterial, not CrLCIB/CrLCIC.
• chloroplast stroma GO:0009570: supported.