phycobilisome rod

cellstructuremech:phycobilisome_rod · Energy complex · Multiprotein complex · Proposed

Peripheral phycobiliprotein cylinder subassembly of a phycobilisome that binds phycobilin chromophores, absorbs excitation energy, and transfers it inward to the allophycocyanin core. [DOI:10.1038/s41467-022-30962-9]

Synonyms: phycobilisome peripheral rod

Part of: phycobilisome (GO:0030089)

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
rod phycobiliproteins	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	cpcA, cpcB	ESSENTIAL	Pigment-binding alpha and beta phycobiliprotein subunits that assemble into peripheral rod disks and absorb incoming light. `DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 resolved a T. vulcanus phycocyanin rod and describe phycobiliprotein alpha and beta subunits with linear tetrapyrrole chromophores as the phycocyanin rod building blocks.
phycobilisome rod linker polypeptides	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	cpcC, cpcD, cpcG	UNKNOWN	Rod-associated linkers stabilize stacked phycobiliprotein disks and tune chromophore energies for transfer from rods toward the allophycocyanin core. `DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 classify T. vulcanus rod, rod-terminal, and rod-core linker proteins and model linker positions in the phycocyanin rod structure.
rod-bound phycobilin chromophores	Small molecule	part of	Reviewed label only (reviewed name; no accession asserted)		ESSENTIAL	Covalently attached linear tetrapyrrole pigments that absorb photons and initiate rod-to-core excitation transfer. `DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 describe phycocyanobilin chromophores covalently bound to the alpha and beta subunits of T. vulcanus phycobilisome rods.

Taxonomic distribution

NCBITaxon:1117 Cyanobacteriota — COMMON: Cyanobacterial hemidiscoidal phycobilisomes contain phycocyanin rods; Kawakami et al. 2022 resolved a T. vulcanus PC rod. [DOI:10.1038/s41467-022-30962-9]
NCBITaxon:2763 Rhodophyta — COMMON: Red algal phycobilisomes include densely packed phycoerythrin rods in block and hemiellipsoidal PBS architectures. [DOI:10.1038/s41467-022-30962-9]

Canonical examples

NCBITaxon:32053 Thermostichus vulcanus — Thermophilic cyanobacterium whose stacked phycocyanin rods were resolved from a light-harvesting phycobilisome preparation. [DOI:10.1038/s41467-022-30962-9]

Functions

photosynthesis, light harvesting GO:0009765 — Phycobilisome rods absorb light in peripheral phycobiliprotein-bound bilins and transfer the resulting excitation inward to the allophycocyanin core.
- DOI:10.1038/s41467-022-30962-9 Kawakami et al. 2022 resolved a light-harvesting phycobilisome rod and describe phycobilisomes as solar-energy-capturing antennae for photosynthetic reaction centers.

Mechanism graphs

Peripheral rods absorb light and transfer excitation to the core (FUNCTION)

Rod phycobiliproteins bind phycobilin chromophores that capture light. Rod linkers stabilize disk stacking and tune the downhill transfer path toward the allophycocyanin core.

Subject	Predicate	Object	Evidence
rod phycobiliproteins	assemble into	phycobilisome rod	`DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 resolved stacked phycocyanin disks in thermophilic cyanobacterial rods.
phycobilisome rod linker polypeptides	stabilize and tune	phycobilisome rod	`DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 classified the rod, rod-terminal, and rod-core linker proteins in T. vulcanus and resolved linker positions in the phycocyanin rod.
rod-bound phycobilin chromophores	are bound by	rod phycobiliproteins	`DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 describe phycocyanobilins covalently bound to the phycocyanin alpha and beta subunits of PBS rods.
phycobilisome rod	transfers excitation to	allophycocyanin core	`DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 discuss excitation movement from PC rods through the allophycocyanin core cylinders toward terminal emitters.
phycobilisome rod	contributes to	photosynthesis, light harvesting	`DOI:10.1038/s41467-022-30962-9` Kawakami et al. 2022 resolved phycocyanin rods from T. vulcanus phycobilisome preparations as light-harvesting subassemblies.

Discussions

CURATION_TODO (OPEN): Resolve exact InterPro, Pfam, NCBIfam, Complex Portal, or ChEBI accessions for phycobilisome rod phycobiliproteins, rod linkers, and bound phycobilins. This first rod child record keeps the mixed rod phycobiliprotein, linker, and chromophore groups reviewed-label-only because a broad phycobiliprotein family would blur rod constituents with core constituents.
INTERPRETATION (RESOLVED): Keep the phycobilisome rod distinct from the whole phycobilisome and from the allophycocyanin core. GO:0030089 denotes the complete phycobilisome. The rod is a peripheral phycobiliprotein subassembly of the complete antenna, while the allophycocyanin core is a different central subassembly that accepts rod excitation.

Evidence

DOI:10.1038/s41467-022-30962-9 Kawakami et al. 2022, Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome, Nature Communications.
GO:0030076 Gene Ontology cellular-component term for the broader light-harvesting complex class.
GO:0030089 Gene Ontology cellular-component term for the containing phycobilisome complex.
GO:0009765 Gene Ontology biological-process term for photosynthesis, light harvesting.
InterPro:IPR012128 InterPro family for phycobilisome alpha/beta subunits; broader than the rod-only phycobiliproteins because it also includes allophycocyanin core subunits.

Curation history

2026-10-03T02:28:59Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-03T02:29:58Z codex · EXPANDED_RECORD — Added light-harvesting-complex parentage, phycobilisome parthood, rod phycobiliprotein/linker/phycobilin components, cyanobacterial and red-algal scope, Thermostichus and Nostoc examples, a light-harvesting function, DOI/GO/InterPro evidence, a nonmechanistic rod light-capture graph, and grounding and boundary discussions.
2026-10-03T02:47:30Z codex · REVIEW_FIXES — Addressed PR #1962 review issue #1963 by moving rod-specific Sui 2021 and Chang 2015 assertions to readable Kawakami 2022 evidence, trimming unsupported cpeA/cpeB gene symbols, and removing the PCC 7120 example.
2026-10-03T02:48:08Z codex · REVIEW_FIXES — Tightened PR #1962 review issue #1963 wording to describe the Kawakami 2022 T. vulcanus structure as a phycocyanin rod resolved from phycobilisome preparations rather than as a rod resolved inside a fully intact phycobilisome.

Source: data/structures/energy_complex/phycobilisome_rod.yaml