carboxysome

GO:0031470 · Microcompartment · Protein shelled organelle · Proposed

A bacterial microcompartment — a polyhedral, selectively permeable protein shell about 100–200 nm across — that encapsulates RuBisCO and carbonic anhydrase to concentrate CO2 around RuBisCO in cyanobacteria and many chemoautotrophs. Alpha-carboxysomes (cso genes) and beta-carboxysomes (ccm genes) evolved their shells and scaffolds independently. [DOI:10.1038/nrmicro.2018.10]

Thin-section electron micrograph of Halothiobacillus neapolitanus cells containing carboxysomes, and negatively stained isolated carboxysomes. Scale bars 100 nm. TEM · *Halothiobacillus neapolitanus* (`NCBITaxon:927`) · Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO; CC BY 3.0, via Wikimedia Commons · CC_BY_3_0 · source: WIKIMEDIA_COMMONS File:Carboxysomes_EM.jpg (M4508748) · `DOI:10.1371/journal.pbio.0050144`

Synonyms: polyhedral body

Xrefs: uniprot.location:SL-0034 — Carboxysome

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
BMC-H shell hexamers (CcmK / CsoS1)	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccmK, csoS1	ESSENTIAL	Tile the shell facets; central pores admit bicarbonate and RuBP. `DOI:10.1038/nrmicro.2018.10` Kerfeld et al. 2018 describe BMC-H hexamers as the main facet tile.
BMC-T shell pseudohexamers (CcmO, CcmP)	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccmO, ccmP	CONDITIONAL	Tandem-BMC-domain paralogues that tile the shell alongside the BMC-H hexamers. Essentiality differs within the set and the field carries the weaker value: UniProt states CcmO is required for carboxysome formation and for recruiting CcmK2, while CcmP is a gated dimer of stacked trimers thought to control metabolite passage rather than to be required for assembly. `PMID:22928045` UniProt cites this paper (P46205) for CcmO being required to recruit the major shell protein CcmK2 to the pre-carboxysome, and for its oligomerisation and interaction with CcmK2. `PMID:24267892` UniProt cites this paper (P46205, P46204) for CcmO's role in carboxysome formation. `PMID:23572529` UniProt cites this paper (Q31QW7) for CcmP forming a dimer of stacked trimers in the shell and for the gating that is thought to control transport of RuBisCO reactants.
BMC-P shell pentamers (CcmL / CsoS4)	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccmL, csoS4A	ESSENTIAL	Cap the vertices of the icosahedral shell. `DOI:10.1038/nrmicro1913` Yeates et al. 2008 assign pentamers to shell vertices.
ribulose-1,5-bisphosphate carboxylase/oxygenase (form I)	Protein complex	part of		rbcL, rbcS, cbbL, cbbS	ESSENTIAL	Encapsulated cargo; fixes CO2 into 3-phosphoglycerate. `PMID:24006469` Rae et al. 2013 review RuBisCO packaging in both carboxysome types.
carboxysomal carbonic anhydrase (CcaA / CsoSCA)	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccaA, csoSCA	ESSENTIAL	Dehydrates bicarbonate to CO2 inside the shell. `DOI:10.1038/nrmicro.2018.10` Kerfeld et al. 2018.
cargo scaffold (CcmM / CsoS2)	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccmM, csoS2	ESSENTIAL	Links RuBisCO to the shell and drives cargo condensation. `PMID:24006469` Rae et al. 2013 describe CcmM and CsoS2 as the RuBisCO-organising proteins.
assembly adaptor CcmN	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ccmN	ESSENTIAL	Bridges cargo to shell: its N-terminus binds the CcmM scaffold, which itself binds RuBisCO, while its C-terminal 18 residues bind the shell protein CcmK2. `PMID:22461622` UniProt cites this paper (P46204) for the CcmN N-terminus interacting with CcmM and its C-terminal 18 residues interacting with CcmK2. `PMID:24267892` UniProt cites this paper (P46204) for CcmN being required for carboxysome formation.
carboxysome positioning system (McdB, with the McdA ATPase)	Protein	acts on	Reviewed label only (reviewed name; no accession asserted)	mcdB	DISPENSABLE	Distributes carboxysomes along the nucleoid. McdB binds the carboxysome and, with the McdA ATPase, sets spacing, size and inheritance; without the system carboxysomes aggregate rather than failing to form. `PMID:30520729` UniProt cites this paper (Q8GJM6) for McdA and McdB together mediating carboxysome spacing, and for McdB self-association and interaction with McdA. `PMID:34406783` UniProt cites this paper (Q8GJM6) for the same distribution role and for preventing carboxysome aggregation.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

BMC-H shell hexamers (CcmK / CsoS1)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q03511`	Carboxysome shell protein CcmK2	ccmK2	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Tile the shell facets; central pores admit bicarbonate and RuBP. `PMID:17675289` Long BM et al. 2007, ‘Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of Q03511, as cited by UniProt. `PMID:20304968` Long BM et al. 2010, ‘Functional cyanobacterial beta-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein’, Plant Physiol. ECO:0000269 experimental evidence for the carboxysome localisation of Q03511, as cited by UniProt. `PMID:22928045` Rae BD et al. 2012, ‘Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL’, PLoS One. ECO:0000269 experimental evidence for the carboxysome localisation of Q03511, as cited by UniProt.
`UniProtKB:Q31RK2`	Carboxysome shell protein CcmK4	ccmK4	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Tile the shell facets; central pores admit bicarbonate and RuBP. `PMID:25117559` Cai F et al. 2015, ‘Engineering bacterial microcompartment shells: chimeric shell proteins and chimeric carboxysome shells’, ACS Synth Biol. ECO:0000269 experimental evidence for the carboxysome localisation of Q31RK2, as cited by UniProt. `PMID:28616951` Faulkner M et al. 2017, ‘Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes’, Nanoscale. ECO:0000269 experimental evidence for the carboxysome localisation of Q31RK2, as cited by UniProt. `PMID:28963440` Niederhuber MJ et al. 2017, ‘Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix’, Mol Biol Cell. ECO:0000269 experimental evidence for the carboxysome localisation of Q31RK2, as cited by UniProt.
`UniProtKB:Q31RK3`	Carboxysome shell protein CcmK3	ccmK3	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (2 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Tile the shell facets; central pores admit bicarbonate and RuBP. `PMID:30389783` Sommer M et al. 2019, ‘Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells’, Plant Physiol. ECO:0000269 experimental evidence for the carboxysome localisation of Q31RK3, as cited by UniProt. `PMID:31048338` Sun Y et al. 2019, ‘Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment’, Plant Cell. ECO:0000269 experimental evidence for the carboxysome localisation of Q31RK3, as cited by UniProt.
`UniProtKB:P45689`	Major carboxysome shell protein CsoS1A	csoS1A	Halothiobacillus neapolitanus c2 (`NCBITaxon:555778`)	REVIEWED
Role and evidence (2 references) The single reviewed UniProtKB entry for gene csoS1, which UniProt lists under the primary name csoS1A, in Halothiobacillus neapolitanus c2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:18258595` Dou Z et al. 2008, ‘CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2.’, J Biol Chem. ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of P45689. `PMID:7934888` English RS et al. 1994, ‘Isolation and characterization of a carboxysome shell gene from Thiobacillus neapolitanus.’, Mol Microbiol. ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of P45689.

BMC-T shell pseudohexamers (CcmO, CcmP)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P46205`	Carboxysome assembly protein CcmO	ccmO	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Tandem-BMC-domain paralogues that tile the shell alongside the BMC-H hexamers; CcmO is required to recruit CcmK2 to the pre-carboxysome, and CcmP forms a gated dimer of stacked trimers thought to control metabolite passage. `PMID:22928045` Rae BD et al. 2012, ‘Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL’, PLoS One. ECO:0000269 experimental evidence for the carboxysome localisation of P46205, as cited by UniProt. `PMID:24267892` Cameron JC et al. 2013, ‘Biogenesis of a bacterial organelle: the carboxysome assembly pathway’, Cell. ECO:0000269 experimental evidence for the carboxysome localisation of P46205, as cited by UniProt. `PMID:31048338` Sun Y et al. 2019, ‘Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment’, Plant Cell. ECO:0000269 experimental evidence for the carboxysome localisation of P46205, as cited by UniProt.
`UniProtKB:Q31QW7`	Carboxysome shell protein CcmP	ccmP	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (1 reference) UniProt annotates this protein to SL-0034 (carboxysome); component role: Tandem-BMC-domain paralogues that tile the shell alongside the BMC-H hexamers; CcmO is required to recruit CcmK2 to the pre-carboxysome, and CcmP forms a gated dimer of stacked trimers thought to control metabolite passage. `PMID:23572529` Cai F et al. 2013, ‘The structure of CcmP, a tandem bacterial microcompartment domain protein from the β-carboxysome, forms a subcompartment within a microcompartment’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of Q31QW7, as cited by UniProt.

BMC-P shell pentamers (CcmL / CsoS4)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q03512`	Carboxysome shell vertex protein CcmL	ccmL	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (2 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Cap the vertices of the icosahedral shell. `PMID:28616951` Faulkner M et al. 2017, ‘Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes’, Nanoscale. ECO:0000269 experimental evidence for the carboxysome localisation of Q03512, as cited by UniProt. `PMID:31048338` Sun Y et al. 2019, ‘Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment’, Plant Cell. ECO:0000269 experimental evidence for the carboxysome localisation of Q03512, as cited by UniProt.
`UniProtKB:O85043`	Carboxysome shell vertex protein CsoS4A	csoS4A	Halothiobacillus neapolitanus c2 (`NCBITaxon:555778`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene csoS4A in Halothiobacillus neapolitanus c2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:19844578` Cai F et al. 2009, ‘The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier.’, PLoS One. ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of O85043.

ribulose-1,5-bisphosphate carboxylase/oxygenase (form I)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q31NB3`	Ribulose bisphosphate carboxylase large chain	cbbL	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Encapsulated cargo; fixes CO2 into 3-phosphoglycerate. `PMID:17675289` Long BM et al. 2007, ‘Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB3, as cited by UniProt. `PMID:20304968` Long BM et al. 2010, ‘Functional cyanobacterial beta-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein’, Plant Physiol. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB3, as cited by UniProt. `PMID:22928045` Rae BD et al. 2012, ‘Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL’, PLoS One. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB3, as cited by UniProt.
`UniProtKB:Q31NB2`	Ribulose bisphosphate carboxylase small subunit	cbbS	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Encapsulated cargo; fixes CO2 into 3-phosphoglycerate. `PMID:17675289` Long BM et al. 2007, ‘Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB2, as cited by UniProt. `PMID:22928045` Rae BD et al. 2012, ‘Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL’, PLoS One. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB2, as cited by UniProt. `PMID:24585024` Nishimura T et al. 2014, ‘In vitro and in vivo analyses of the role of the carboxysomal β-type carbonic anhydrase of the cyanobacterium Synechococcus elongatus in carboxylation of ribulose-1,5-bisphosphate’, Photosynth Res. ECO:0000269 experimental evidence for the carboxysome localisation of Q31NB2, as cited by UniProt.

carboxysomal carbonic anhydrase (CcaA / CsoSCA)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P27134`	Carbonic anhydrase	ccaA	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Dehydrates bicarbonate to CO2 inside the shell. `PMID:17675289` Long BM et al. 2007, ‘Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of P27134, as cited by UniProt. `PMID:20304968` Long BM et al. 2010, ‘Functional cyanobacterial beta-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein’, Plant Physiol. ECO:0000269 experimental evidence for the carboxysome localisation of P27134, as cited by UniProt. `PMID:22928045` Rae BD et al. 2012, ‘Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL’, PLoS One. ECO:0000269 experimental evidence for the carboxysome localisation of P27134, as cited by UniProt.

cargo scaffold (CcmM / CsoS2)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q03513`	Carboxysome assembly protein CcmM	ccmM	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (3 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Links RuBisCO to the shell and drives cargo condensation. `PMID:17675289` Long BM et al. 2007, ‘Analysis of carboxysomes from Synechococcus PCC7942 reveals multiple Rubisco complexes with carboxysomal proteins CcmM and CcaA’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of Q03513, as cited by UniProt. `PMID:20304968` Long BM et al. 2010, ‘Functional cyanobacterial beta-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein’, Plant Physiol. ECO:0000269 experimental evidence for the carboxysome localisation of Q03513, as cited by UniProt. `PMID:28616951` Faulkner M et al. 2017, ‘Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes’, Nanoscale. ECO:0000269 experimental evidence for the carboxysome localisation of Q03513, as cited by UniProt.
`UniProtKB:O85041`	Carboxysome assembly protein CsoS2B	csoS2	Halothiobacillus neapolitanus c2 (`NCBITaxon:555778`)	REVIEWED
Role and evidence (3 references) The single reviewed UniProtKB entry for gene csoS2 in Halothiobacillus neapolitanus c2, a taxon this record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:10525740` Baker SH et al. 1999, ‘The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in thiobacillus neapolitanus.’, Arch Microbiol. ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of O85041. `PMID:18258595` Dou Z et al. 2008, ‘CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2.’, J Biol Chem. ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of O85041. `PMID:25826651` Cai F et al. 2015, ‘Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component.’, Life (Basel). ECO:0000269 experimental evidence cited by UniProt for the 'Carboxysome' localisation of O85041.

assembly adaptor CcmN

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P46204`	Carboxysome assembly protein CcmN	ccmN	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (2 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Bridges cargo to shell: its N-terminus binds the CcmM scaffold, which itself binds RuBisCO, while its C-terminal 18 residues bind the shell protein CcmK2. `PMID:22461622` Kinney JN et al. 2012, ‘Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly’, J Biol Chem. ECO:0000269 experimental evidence for the carboxysome localisation of P46204, as cited by UniProt. `PMID:31048338` Sun Y et al. 2019, ‘Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment’, Plant Cell. ECO:0000269 experimental evidence for the carboxysome localisation of P46204, as cited by UniProt.

carboxysome positioning system (McdB, with the McdA ATPase)

Accession	Protein	Gene	Organism	Entry
`UniProtKB:Q8GJM6`	Maintenance of carboxysome distribution protein B	mcdB	Synechococcus elongatus PCC 7942 (`NCBITaxon:1140`)	REVIEWED
Role and evidence (2 references) UniProt annotates this protein to SL-0034 (carboxysome); component role: Distributes carboxysomes along the nucleoid. McdB binds the carboxysome and, with the McdA ATPase, sets spacing, size and inheritance; without the system carboxysomes aggregate rather than failing to form. `PMID:30520729` MacCready JS et al. 2018, ‘Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria’, Elife. ECO:0000269 experimental evidence for the carboxysome localisation of Q8GJM6, as cited by UniProt. `PMID:34406783` Hakim P et al. 2021, ‘Dissection of the ATPase active site of McdA reveals the sequential steps essential for carboxysome distribution’, Mol Biol Cell. ECO:0000269 experimental evidence for the carboxysome localisation of Q8GJM6, as cited by UniProt.

Taxonomic distribution

NCBITaxon:1117 Cyanobacteriota — UNIVERSAL: Cyanobacteria. Beta-carboxysomes in most lineages; alpha-carboxysomes in marine Prochlorococcus and some Synechococcus. [PMID:24006469]
NCBITaxon:1224 Pseudomonadota — VARIABLE: Alpha-carboxysomes in many chemoautotrophs (Halothiobacillus, Thiomicrospira, Nitrosomonas). [PMID:24006469]

Canonical examples

NCBITaxon:1140 Synechococcus elongatus PCC 7942 — Model for beta-carboxysomes. [PMID:24006469]
NCBITaxon:927 Halothiobacillus neapolitanus — Model for alpha-carboxysomes. [PMID:24006469]

Functions

carbon dioxide concentrating mechanism — Raises the CO2 concentration at RuBisCO and limits O2 access, suppressing photorespiration.
- DOI:10.1038/nrmicro.2018.10 Kerfeld et al. 2018.
carbon fixation GO:0015977
- PMID:24006469 Rae et al. 2013.

Associated traits

CONFERS traitmech:000072 — carboxysome carboxysome — TraitMech models carboxysome possession as a morphology trait; this record models the organelle.
- DOI:10.1038/nrmicro.2018.10 Kerfeld et al. 2018 describe the carboxysome as the archetypal bacterial microcompartment; TraitMech records possession of it as the morphology trait traitmech:000072.

Physical properties

DIAMETER: 100-200 UO:0000018 [DOI:10.1038/nrmicro.2018.10]

Mechanism graphs

The shell and carbonic anhydrase concentrate CO2 at RuBisCO (FUNCTION)

Subject	Predicate	Object	Evidence
carboxysome shell	permits passage of	bicarbonate	`DOI:10.1038/nrmicro.2018.10` Shell pores are selective for small anions such as HCO3-.
carbonic anhydrase	converts	bicarbonate	`DOI:10.1038/nrmicro.2018.10` Kerfeld et al. 2018.
carbonic anhydrase	elevates local concentration of	carbon dioxide	`PMID:24006469` Rae et al. 2013.
carboxysome shell	prevents loss of	carbon dioxide	`DOI:10.1038/nrmicro.2018.10` The shell retards CO2 efflux to the cytoplasm.
carbon dioxide	substrate of	RuBisCO	`PMID:24006469` Rae et al. 2013.
RuBisCO	catalyses `RO:0002327`	carbon fixation	`PMID:24006469` Rae et al. 2013.

Cargo condenses on a scaffold, an adaptor recruits the shell, and the shell closes around it (ASSEMBLY)

Beta-carboxysome assembly order, and the placement step that follows it.

Subject	Predicate	Object	Evidence
CcmM scaffold	binds	RuBisCO	`PMID:24006469` Rae et al. 2013 describe CcmM and CsoS2 as the RuBisCO-organising proteins of the two carboxysome types.
CcmM scaffold	forms	pre-carboxysome cargo condensate	`PMID:24006469` Rae et al. 2013 describe cargo condensation preceding shell encapsulation in beta-carboxysomes.
CcmN adaptor	bridges	CcmM scaffold	`PMID:22461622` UniProt cites this paper (P46204) for the CcmN N-terminus interacting with CcmM.
CcmN adaptor	recruits	BMC-H shell hexamers	`PMID:22461622` UniProt cites this paper (P46204) for the CcmN C-terminal 18 residues interacting with CcmK2.
BMC-T shell pseudohexamers (CcmO, CcmP)	recruits	BMC-H shell hexamers	`PMID:22928045` UniProt cites this paper (P46205) for CcmO being required to recruit CcmK2.
BMC-H shell hexamers	forms	carboxysome shell	`DOI:10.1038/nrmicro.2018.10` Kerfeld et al. 2018 describe BMC-H hexamers tiling the shell facets.
BMC-T shell pseudohexamers (CcmO, CcmP)	forms	carboxysome shell	`PMID:23572529` UniProt cites this paper (Q31QW7) for CcmP forming a dimer of stacked trimers within the shell.
carboxysome shell	encapsulates	pre-carboxysome cargo condensate	`PMID:24006469` Rae et al. 2013 describe the shell closing around the condensed cargo.
McdB positioning system	drives	carboxysome spacing along the nucleoid	`PMID:30520729` UniProt cites this paper (Q8GJM6) for McdA and McdB together mediating carboxysome spacing.

Discussions

CURATION_TODO (RESOLVED): Should the RuBisCO assembly chaperone RbcX (Q31N04) be a carboxysome component? The UniProt Subcellular Location seeding reported RbcX as annotated to the carboxysome with no matching component. It is an RbcL-specific folding chaperone whose homodimer binds the exposed C-terminus of an RbcL monomer during assembly; it is not part of the assembled structure. Recording the decision so the next seeding run does not re-raise it.

Evidence

DOI:10.1038/nrmicro.2018.10 Kerfeld et al. 2018, "Bacterial microcompartments".
DOI:10.1038/nrmicro1913 Yeates et al. 2008, "Protein-based organelles in bacteria".
PMID:24006469 Rae et al. 2013, "Functions, compositions, and evolution of the two types of carboxysomes".

Curation history

2026-08-29T00:00:00Z claude · CREATED_RECORD — Drafted from the cited reviews, aligned with the TraitMech carboxysome trait record (traitmech:000072). Not yet human-reviewed.
2026-08-29T01:00:00Z claude · FIX_REVIEW_FINDINGS — PR #1 review: NCBITaxon:1117 label updated to the current name Cyanobacteriota (#5).
2026-08-29T02:00:00Z claude · ADD_IMAGE — Added Commons image File:Carboxysomes_EM.jpg (CC BY 3.0, Tsai et al. 2007 DOI:10.1371/journal.pbio.0050144, NCBITaxon:927) as the #15 canary; licence, attribution and taxon verified against the Commons/Wikidata APIs at retrieval.
2026-08-30T02:14:16Z uniprot_sl · SEED_PROTEIN_EXAMPLES — Added 8 taxon-paired protein example(s) from UniProtKB reviewed entries annotated to SL-0034 (Carboxysome), matched to components by gene symbol, each carrying UniProt's ECO:0000269 PubMed evidence for the localisation.
2026-08-30T02:14:17Z uniprot_sl · ADD_UNIPROT_SL_XREF — Added uniprot.location:SL-0034 (Carboxysome); mapping read from the GO line of UniProt subcell.txt.
2026-08-30T19:08:31Z fetch_commons_image · ADD_IMAGE — Updated Commons image File:Carboxysomes_EM.jpg (CC_BY_3_0, Halothiobacillus neapolitanus); licence, attribution and taxon read from the Commons and Wikidata APIs at retrieval.
2026-08-30T19:11:11Z fetch_commons_image · ADD_IMAGE — Updated Commons image File:Carboxysomes_EM.jpg (CC_BY_3_0, Halothiobacillus neapolitanus); licence, attribution and taxon read from the Commons and Wikidata APIs at retrieval.
2026-08-30T19:19:18Z claude · ADD_COMPONENTS — Added the components the UniProt SL seeding found unmatched (#40): BMC-T shell pseudohexamers (CcmO, CcmP), the CcmN assembly adaptor, and the McdB positioning system, each with the papers UniProt attributes the claim to. Declined RbcX with a recorded reason: it is a RuBisCO folding chaperone, not part of the assembled structure.
2026-08-30T19:19:33Z uniprot_sl · SEED_PROTEIN_EXAMPLES — Added 4 taxon-paired protein example(s) from UniProtKB reviewed entries annotated to SL-0034 (Carboxysome), matched to components by gene symbol, each carrying UniProt's ECO:0000269 PubMed evidence for the localisation.
2026-08-31T04:03:50Z claude · ADD_ASSEMBLY_GRAPH — Review of PR #60: added the ASSEMBLY graph the new components belonged in (#67) — cargo condensation on CcmM, CcmN bridging cargo to shell, CcmO recruiting CcmK2, shell closure, and McdB-driven spacing — and stated in the bmc_t role that essentiality differs between CcmO and CcmP (#68).
2026-08-31T04:09:18Z claude · ADD_TRAIT_EVIDENCE — TraitLink.evidence became required in the schema; cited the review already backing the record for the carboxysome trait link.
2026-08-31T06:12:34Z claude · SET_COMPONENT_ROLE — component_role became required (#77) so the constituent/machinery distinction is machine-readable rather than prose. Set per component; ASSOCIATED_MACHINERY only where the protein acts on the already-assembled structure.
2026-09-02T05:45:20Z interpro_groundings · GROUND_COMPONENTS — Applied exact integrated InterPro family groundings to none; recorded label-only decisions for bmc_h, bmc_p, carbonic_anhydrase, scaffold, assembly_adaptor, positioning. The fixed reviewed allow-list required exact component identity, reviewed UniProt examples, type=family entries, and unchanged family consensus across curated scope examples.
2026-09-02T23:27:08Z uniprot_sl · ENRICH_EVIDENCE_NOTES — #41: added the cited paper's author, year, title and journal to 30 UniProt-seeded evidence note(s), fetched from PubMed esummary. The notes were previously identical per accession, so a reader could not tell the cited papers apart. Only notes byte-identical to the seeded boilerplate were touched.
2026-09-04T01:40:08Z codex · ENHANCE_CAUSAL_GRAPH — Added descriptions to the remaining carboxysome CO2-concentrating and assembly graph edges so every causal edge now states its mechanism.
2026-09-08T07:39:38Z uniprot_genes · SEED_PROTEIN_EXAMPLES — #183: added 3 protein example(s) by resolving each of the component's declared gene symbols to the single reviewed UniProtKB entry for that symbol in a taxon this record names, deduplicated by accession. Symbols resolving to more than one reviewed entry were skipped rather than chosen between.
2026-09-21T12:34:04Z codex · REPLACED_UNREADABLE_EVIDENCE — Resolved #1241 by routing Rae et al. 2013 carboxysome review evidence through reachable PMID:24006469 instead of the unreadable MMBR DOI.

Source: data/structures/microcompartment/carboxysome.yaml