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

Components

Component	Type	Genes	Essential	Role
BMC-H shell hexamers (CcmK / CsoS1)	PROTEIN	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-P shell pentamers (CcmL / CsoS4)	PROTEIN	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	rbcL, rbcS, cbbL, cbbS	ESSENTIAL	Encapsulated cargo; fixes CO2 into 3-phosphoglycerate. `DOI:10.1128/MMBR.00061-12` Rae et al. 2013 review RuBisCO packaging in both carboxysome types.
carboxysomal carbonic anhydrase (CcaA / CsoSCA)	PROTEIN	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	ccmM, csoS2	ESSENTIAL	Links RuBisCO to the shell and drives cargo condensation. `DOI:10.1128/MMBR.00061-12` Rae et al. 2013 describe CcmM and CsoS2 as the RuBisCO-organising proteins.

Taxonomic distribution

NCBITaxon:1117 Cyanobacteriota — UNIVERSAL: Cyanobacteria. Beta-carboxysomes in most lineages; alpha-carboxysomes in marine Prochlorococcus and some Synechococcus. [DOI:10.1128/MMBR.00061-12]
NCBITaxon:1224 Pseudomonadota — VARIABLE: Alpha-carboxysomes in many chemoautotrophs (Halothiobacillus, Thiomicrospira, Nitrosomonas). [DOI:10.1128/MMBR.00061-12]

Canonical examples

NCBITaxon:1140 Synechococcus elongatus PCC 7942 — Model for beta-carboxysomes. [DOI:10.1128/MMBR.00061-12]
NCBITaxon:927 Halothiobacillus neapolitanus — Model for alpha-carboxysomes. [DOI:10.1128/MMBR.00061-12]

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
- DOI:10.1128/MMBR.00061-12 Rae et al. 2013.

Associated traits

CONFERS traitmech:000072 carboxysome — TraitMech models carboxysome possession as a morphology trait; this record models the organelle.

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	`DOI:10.1128/MMBR.00061-12` 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	`DOI:10.1128/MMBR.00061-12` Rae et al. 2013.
RuBisCO	catalyses `RO:0002327`	carbon fixation	`DOI:10.1128/MMBR.00061-12` Rae et al. 2013.

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".
DOI:10.1128/MMBR.00061-12 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.

Source: data/structures/microcompartment/carboxysome.yaml