chloroplast stroma

GO:0009570 · Membrane organelle · Subcellular region · Proposed

The internal space enclosed by the chloroplast double membrane but excluding the thylakoid space. [GO:0009570]

Synonyms: chloroplastic stroma

Part of: chloroplast (GO:0009507)

Has part: chloroplast nucleoid (GO:0042644); plastoglobule (GO:0010287)

Xrefs: uniprot.location:SL-0055 — Chloroplast stroma

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

Taxonomic distribution

NCBITaxon:33090 Viridiplantae — COMMON: Chloroplast stroma occurs in chloroplast-bearing green algae and land plants as the internal matrix compartment inside the chloroplast envelope. [DOI:10.1098/rstb.2009.0103]
NCBITaxon:3055 Chlamydomonas reinhardtii — COMMON: The Chlamydomonas chloroplast proteome includes stromal metabolic and protein-biogenesis pathways in a unicellular green-algal model. [DOI:10.1007/s00294-011-0339-1]

Canonical examples

NCBITaxon:3055 Chlamydomonas reinhardtii — Unicellular green alga whose chloroplast stroma contains nucleoids and metabolic enzymes characterized in chloroplast proteome surveys. [DOI:10.1007/s00294-011-0339-1]

Functions

protein import into chloroplast stroma GO:0045037 — Imported nucleus-encoded chloroplast precursor proteins cross the outer and inner envelope membranes to enter the chloroplast stroma.
- GO:0045037 GO:0045037 defines protein import into the chloroplast stroma as transport from the cytosol into the stroma.
- DOI:10.1016/j.cell.2022.10.030 Jin et al. 2022 resolved a Chlamydomonas TOC-TIC supercomplex spanning the chloroplast envelope.

Mechanism graphs

Chloroplast stroma topology and import (FUNCTION)

The chloroplast envelope encloses the stroma, stromal protein import terminates in the stroma after precursor transit across the envelope, and chloroplast nucleoids and plastoglobules occupy the stromal compartment.

Subject	Predicate	Object	Evidence
chloroplast envelope	encloses	chloroplast stroma	`GO:0009570` GO:0009570 defines the stroma as the chloroplast internal space enclosed by the double membrane.
chloroplast nucleoid	is part of	chloroplast stroma	`DOI:10.1093/mp/ssp083` Karcher et al. 2009 assayed Chlamydomonas chloroplast DNA organization as HLP-containing nucleoids.
plastoglobule	is part of	chloroplast stroma	`uniprot.location:SL-0217` — Plastoglobule UniProt SL-0217 describes plastoglobules as lipid-containing structures in the chloroplast stroma.
protein import into chloroplast stroma	terminates in	chloroplast stroma	`GO:0045037` GO:0045037 defines protein import into the chloroplast stroma as transport from the cytosol into the stroma. `DOI:10.1016/j.cell.2022.10.030` Jin et al. 2022 resolved a Chlamydomonas TOC-TIC supercomplex spanning both chloroplast envelope membranes.

Discussions

INTERPRETATION (RESOLVED): Keep the chloroplast stroma separate from thylakoid lumen compartments. GO:0009570 denotes the hydrophilic internal matrix enclosed by the chloroplast envelope, explicitly excluding the thylakoid space that has dedicated chloroplast and plastid lumen terms.

Evidence

GO:0009570 Gene Ontology cellular-component term for the chloroplast stroma.
GO:0009532 Gene Ontology cellular-component term for plastid stroma.
GO:0009507 Gene Ontology cellular-component term for the containing chloroplast.
GO:0009941 Gene Ontology cellular-component term for the chloroplast envelope that encloses the stroma.
GO:0042644 Gene Ontology cellular-component term for chloroplast nucleoid.
GO:0010287 Gene Ontology cellular-component term for plastoglobule.
GO:0009543 Gene Ontology cellular-component term for chloroplast thylakoid lumen, which is separate from the stroma.
GO:0045037 Gene Ontology biological-process term for protein import into the chloroplast stroma.
uniprot.location:SL-0055 — Chloroplast stroma UniProt Subcellular Location SL-0055 maps Chloroplast stroma to GO:0009570 and places it under the Chloroplast location.
DOI:10.1098/rstb.2009.0103 Keeling 2010, The endosymbiotic origin, diversification and fate of plastids, Philosophical Transactions of the Royal Society B.
DOI:10.1007/s00294-011-0339-1 Terashima, Specht and Hippler 2011, The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features, Current Genetics.
uniprot.location:SL-0217 — Plastoglobule UniProt Subcellular Location entry SL-0217 describes the plastoglobule as a lipid-containing structure in the chloroplast stroma.
DOI:10.1093/mp/ssp083 Karcher et al. 2009, The Chlamydomonas Chloroplast HLP Protein Is Required for Nucleoid Organization and Genome Maintenance, Molecular Plant.
DOI:10.1016/j.cell.2022.10.030 Jin et al. 2022, Structure of a TOC-TIC supercomplex spanning two chloroplast envelope membranes, Cell.

Curation history

2026-09-13T01:20:34Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-13T01:22:26Z codex · EXPANDED_RECORD — Added the UniProt SL xref and exact synonym, plastid-stroma parentage, chloroplast parthood, chloroplast nucleoid and plastoglobule parts, Chlamydomonas and Viridiplantae scope, stromal protein-import evidence, a nonmechanistic topology/import graph, and a thylakoid-lumen boundary discussion.
2026-09-13T01:29:18Z codex · ADDRESS_REVIEW — Resolved #731 by retargeting the import graph edge to the GO:0045037 process endpoint, and resolved #732 by replacing circular plastoglobule parthood support with direct UniProt SL-0217 evidence.

Source: data/structures/membrane_organelle/chloroplast_stroma.yaml