LCIC (low-CO2-inducible protein C; Cre06.g307500) is a soluble chloroplast stromal protein of Chlamydomonas reinhardtii and the closest paralog of LCIB. Both belong to the LCIB/LCIC family (Pfam PF18599), whose members fold like beta-carbonic anhydrases. LCIC is induced when CO2 is limiting and associates tightly with LCIB in a high-molecular-weight complex (about 350 to 440 kDa, roughly 1:1 LCIB:LCIC, probably hexameric). Under limiting CO2 in the light this complex gathers as puncta around the pyrenoid, outside the starch sheath, and it disperses through the stroma when CO2 is high or in the dark. The crystal structure of the LCIC core (residues 40-344) shows a beta-CA fold with one zinc ion per subunit, held by the canonical Cys-His-Cys triad (Cys119, His179, Cys203). The His and Arg residues that are essential for catalysis in active homologs are disordered. Recombinant LCIC, the recombinant LCIB-LCIC complex and the native complex purified from algal cells showed no carbonic anhydrase activity in vitro. LCIB, but not LCIC, has since been shown to complement carbonic anhydrase-deficient yeast and Arabidopsis mutants. So the catalytic contribution of LCIC is unresolved. LCIC is needed for LCIB to move to the pyrenoid periphery, and in an lcib mutant LCIC does not accumulate. The LCIB/LCIC complex is thought to recapture CO2 leaking from the pyrenoid as bicarbonate, or to act as a diffusion barrier. LCIC also interacts with the bestrophin-like proteins LCI11 and Cre16.g662600.
Definition: A chloroplast stromal protein complex of the beta-carbonic-anhydrase-like proteins LCIB and LCIC, about 350 to 440 kDa and probably hexameric. Under limiting CO2 it relocates to the periphery of the pyrenoid. Found in green algae with a pyrenoid-based CO2-concentrating mechanism.
Justification: The complex is well established by Y2H, co-IP, gel filtration, co-expression and affinity-purification/MS. There is no GO complex term for it, so LCIC can only be placed in the generic GO:0032991.
Parent term: protein-containing complex
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009570 chloroplast stroma | IDA PMID:28938113 A Spatial Interactome Reveals the Protein Organization of th... | NEW | Summary: LCIC is a soluble chloroplast stromal protein. LCIC-mCherry forms puncta at the pyrenoid periphery that co-localize with LCIB and lie outside the starch sheath. GOA currently has no annotations for LCIC. Reason: Direct localization of tagged LCIC (Mackinder et al. 2017) together with the earlier co-localization of LCIB and LCIC near the pyrenoid (Yamano et al. 2010) supports chloroplast stroma. The puncta sit outside the STA2 starch plates, so the protein is stromal at the pyrenoid periphery and not inside the pyrenoid matrix. I therefore do not propose GO:1990732 pyrenoid. This is the location the module gives for the LCIB/LCIC annoton. Supporting Evidence: PMID:28938113 Our data confirm that LCIB and LCIC, known stromal soluble proteins, are in a tight complex PMID:28938113 LCIB and LCIC were co-localized (Figure 4D) PMID:28938113 STA2 was localized within the perimeter described by LCIC PMID:20660228 LCIB and LCIC are co-localized in the vicinity of the pyrenoid under LC conditions in the light, forming a hexamer complex of approximately 350 kDa |
| GO:0008270 zinc ion binding | IDA PMID:27911826 Structural insights into the LCIB protein family reveals a n... | NEW | Summary: The 2.51 A crystal structure of LCIC (PDB 5B5X, residues 40-344) shows one Zn2+ per subunit. It is coordinated by Cys119, His179 and Cys203, the canonical beta-CA zinc ligands. Reason: The structure directly shows zinc bound to LCIC (UniProt BINDING features at residues 119, 179 and 203 from PDB 5B5X). This is a well-supported structural property. I keep it as a non-core feature, because there is no evidence that zinc supports catalysis in LCIC; the protein was catalytically inactive in vitro. Supporting Evidence: PMID:27911826 We determined the crystal structures of LCIB and limiting CO2-inducible C protein (LCIC) from C. reinhardtii and a CA-functional homolog from Phaeodactylum tricornutum, all of which harbor motifs bearing close resemblance to the active site of canonical Ξ²-CAs PMID:34791500 the crystalline structures of these proteins resemble that of Ξ²-type carbonic anhydrase (CA), which possesses an active CA site that coordinates with a zinc ion |
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Download this section (compressed HTML)Q: Is LCIC a catalytic or a regulatory/structural subunit of the LCIB/LCIC complex? Should the module's carbonate dehydratase activity (GO:0004089) be asserted for LCIB alone, with LCIC recorded only as a complex member, until LCIC-containing complexes are shown to be active?
Suggested experts: Fukuzawa H, Yamano T, Mueller-Cajar O
Q: Does phosphorylation at LCIC Ser160, next to the disordered active-site His161, switch the complex between inactive and active states?
Q: What is the functional significance of the LCIC interaction with the bestrophin-like proteins LCI11 and Cre16.g662600? Is the LCIB/LCIC complex positioned next to the thylakoid bicarbonate channels?
Suggested experts: Mackinder LCM
Experiment: Test LCIC alone and LCIB+LCIC co-expression for complementation of the yeast nce103 and Arabidopsis beta-ca5 mutants, as already done for LCIB. Include zinc-ligand (C119A/H179A/C203A) LCIC variants, and measure CA activity of native complex purified from very-low-CO2 cells under reducing and phosphorylation-preserving conditions.
Hypothesis: LCIC contributes catalytic carbonic anhydrase activity to the LCIB/LCIC complex under the right conditions.
Type: genetic complementation and enzyme assay
Experiment: Generate an lcic null mutant (CRISPR or CLiP insertion) and measure growth at air and very low CO2, photosynthetic Ci affinity, and LCIB abundance and localization. Then complement with wild-type or zinc-site-mutant LCIC.
Hypothesis: LCIC is required for CCM function independently of its role in stabilizing and relocating LCIB.
Type: mutant phenotyping and complementation
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