pyrenoid

GO:1990732 · Other · Other · Proposed

A non-membrane-bounded organelle found within the chloroplasts of algae and hornworts; responsible for carbon dioxide fixation. [GO:1990732]

Part of: chloroplast (GO:0009507)

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

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
ribulose bisphosphate carboxylase complex	Protein complex	part of	`GO:0048492`			ESSENTIAL	Ribulose-1,5-bisphosphate carboxylase/oxygenase complexes densely concentrated in the pyrenoid matrix to fix CO2. `DOI:10.1016/j.cell.2017.08.008` Freeman Rosenzweig et al. 2017 characterized the Chlamydomonas reinhardtii pyrenoid as a Rubisco-rich, non-membrane-bound, liquid-like organelle. `DOI:10.1073/pnas.1522866113` Mackinder et al. 2016 showed that EPYC1 links Rubisco in the Chlamydomonas pyrenoid matrix.
EPYC1 Rubisco linker	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	EPYC1		CONDITIONAL	Intrinsically disordered Chlamydomonas matrix linker that multivalently binds Rubisco holoenzymes and drives their phase separation into a pyrenoid-like condensate. `DOI:10.1073/pnas.1522866113` Mackinder et al. 2016 identified EPYC1 as a repeat protein that binds Rubisco and links Rubisco complexes to form the pyrenoid. `DOI:10.1038/s41467-018-07624-w` Wunder et al. 2018 showed that Chlamydomonas EPYC1 and Rubisco can phase-separate into liquid droplets in vitro.

Taxonomic distribution

NCBITaxon:2759 Eukaryota — RARE: Pyrenoids are non-membrane-bound chloroplast organelles found across most eukaryotic algae and in the hornwort land-plant lineage, not throughout Eukaryota. [DOI:10.1093/plcell/koad157]
NCBITaxon:3055 Chlamydomonas reinhardtii — COMMON: The Chlamydomonas pyrenoid has a Rubisco/EPYC1 matrix and is a genetically tractable model for the algal carbon-concentrating mechanism. [DOI:10.1016/j.cell.2017.08.044]

Canonical examples

NCBITaxon:3055 Chlamydomonas reinhardtii — Green alga in which EPYC1 was tied to Rubisco matrix assembly, pyrenoid inheritance, and liquid-like pyrenoid organization. [DOI:10.1016/j.cell.2017.08.008]

Functions

carbon fixation GO:0015977 — The pyrenoid concentrates Rubisco so CO2 can be fixed by the Calvin-Benson-Bassham cycle in the chloroplast.
- DOI:10.1016/j.cell.2017.08.008 Freeman Rosenzweig et al. 2017 describe the pyrenoid as the algal CO2-fixing organelle and tracked its Rubisco-rich matrix during cell division.
- DOI:10.1093/plcell/koad157 He, Crans, and Jonikas 2023 review the pyrenoid as the eukaryotic CO2-concentrating organelle.

Mechanism graphs

EPYC1 crosslinks Rubisco to assemble a pyrenoid matrix (ASSEMBLY)

In Chlamydomonas, the intrinsically disordered EPYC1 linker binds Rubisco holoenzymes multivalently, forming a phase-separated matrix that concentrates Rubisco inside the chloroplast pyrenoid.

Subject	Predicate	Object	Evidence
EPYC1 Rubisco linker	binds	ribulose bisphosphate carboxylase complex	`DOI:10.1073/pnas.1522866113` Mackinder et al. 2016 identified EPYC1 as a repeat protein that links Rubisco.
EPYC1 Rubisco linker	multivalently crosslinks	ribulose bisphosphate carboxylase complex	`DOI:10.1038/s41467-018-07624-w` Wunder et al. 2018 showed that purified EPYC1 and Rubisco are sufficient for liquid-droplet formation in vitro.
multivalent EPYC1-Rubisco network	phase-separates into	pyrenoid matrix	`DOI:10.1016/j.cell.2017.08.008` Freeman Rosenzweig et al. 2017 measured liquid-like organization and dynamic reorganization of the Chlamydomonas pyrenoid. `DOI:10.1038/s41467-018-07624-w` Wunder et al. 2018 reconstituted the EPYC1/Rubisco phase separation mechanism.
pyrenoid matrix	concentrates	ribulose bisphosphate carboxylase complex	`DOI:10.1016/j.cell.2017.08.044` Mackinder et al. 2017 spatially organized algal CO2-concentrating mechanism proteins around the Rubisco pyrenoid matrix.
ribulose bisphosphate carboxylase complex	catalyses `RO:0002327`	carbon fixation	`DOI:10.1093/plcell/koad157` He, Crans, and Jonikas 2023 review pyrenoid Rubisco concentration as a core feature of the eukaryotic CO2-concentrating mechanism.

Discussions

CURATION_TODO (OPEN): Resolve an exact source-neutral grounding for the EPYC1 Rubisco-linker family or for functionally equivalent pyrenoid Rubisco-linker proteins. This first pyrenoid record keeps EPYC1 label-only because EPYC1 is a Chlamydomonas matrix linker and was not matched to a taxon-agnostic family CURIE.

Evidence

DOI:10.1016/j.cell.2017.08.008 Freeman Rosenzweig et al. 2017, The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization, Cell.
DOI:10.1073/pnas.1522866113 Mackinder et al. 2016, A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle, PNAS.
DOI:10.1038/s41467-018-07624-w Wunder et al. 2018, The phase separation underlying the pyrenoid-based microalgal Rubisco supercharger, Nature Communications.
DOI:10.1016/j.cell.2017.08.044 Mackinder et al. 2017, A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism, Cell.
DOI:10.1093/plcell/koad157 He, Crans, and Jonikas 2023, The pyrenoid: the eukaryotic CO2-concentrating organelle, Plant Cell.

Curation history

2026-09-10T06:59:09Z claude · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-10T07:00:26Z claude · EXPANDED_RECORD — Added GO non-membrane-bounded-organelle parentage and chloroplast parthood, Rubisco and EPYC1 components, Eukaryota and Chlamydomonas taxonomic scope, a carbon fixation function, record-level evidence, an EPYC1/Rubisco matrix assembly graph, and an EPYC1 grounding TODO.
2026-09-10T07:09:25Z claude · FIXED_GROUNDING_LABELS — Aligned GO:0048492 Rubisco component and graph labels with the canonical GO label, and removed GO:1990732 from the narrower pyrenoid matrix graph node.
2026-09-10T07:25:56Z claude · ADDRESS_REVIEW — Resolved #331 by removing the overbroad GO:0160223 pyrenoid tubule has_part assertion; resolved #332 by removing the assembly-stage Rubisco matrix phase-separation item from top-level functions.
2026-09-20T21:51:50Z codex · ADDRESSED_REVIEW — Retyped the GO-grounded ribulose bisphosphate carboxylase complex graph node from GENE_OR_PROTEIN to STRUCTURE.

Source: data/structures/other/pyrenoid.yaml