Vacuolar sorting receptor cycle in plants

Soluble hydrolases bound for the plant lytic vacuole carry sorting signals that vacuolar sorting receptors (VSRs) recognise at the trans-Golgi network and prevacuolar compartment. The receptor-cargo complex travels to the prevacuolar compartment, where cargo is released, and the retromer complex of Vps35, Vps26 and Vps29 returns the receptors for another round. This module is the green-lineage form of that cycle.

MODULE:plant_vacuolar_sorting_receptor_cycleDRAFTCONCRETEBiological Processmodules/plant_vacuolar_sorting_receptor_cycle.yaml
protein targeting to vacuoleGO:0006623 retromer complexGO:0030904

Viridiplantae scope, with Arabidopsis representatives. Read as a satisfiability rule, a genome needs a VSR and the three retromer subunits; RMRs, which act on the storage-vacuole route, are optional. The VSR selector lists both UniProt's and PANTHER's own placements, because the two disagree (see that step). Several selectors come from PANTHER's release-19 Arabidopsis classification file, because the local entries tables list Vps29 without a subfamily. The retromer selectors are not plant-specific (Vps35 SF0, the whole Vps26 family and Vps29 SF12), and the VSR step is also met by animal PRADC1, so outside plants the module is met by any genome with retromer and a PRADC1 protein, including human; the rule is meant for plant genomes only. Within plants the VSR selectors are narrow: the UniProt-placed subfamilies list Arabidopsis and pea and the PANTHER-file ones Arabidopsis and poplar, so other green lineages may fail the VSR step for want of a selector. Not modelled: the sorting nexins and the Rab7 and Rab5 GTPases that regulate the cycle (the Rab7 step is in plant_vacuole_fusion), and the receptor-independent routes to the vacuole.

4Nodes
3Parts
0Variant Sets
0Variants
5Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:plant_vacuolar_sorting_receptor_cycle deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

0 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (8 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
retromer_vps35 VPS35A (Arabidopsis)
UniProtKB:Q7X659
Family Representative 		cargo adaptor activity
GO:0140312 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
retromer_vps35 VPS35B (Arabidopsis)
UniProtKB:F4I0P8
Family Representative 		cargo adaptor activity
GO:0140312 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
retromer_vps35 VPS35C (Arabidopsis)
UniProtKB:A8R7K9
Family Representative 		cargo adaptor activity
GO:0140312 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
retromer_vps29 VPS29 (Arabidopsis)
UniProtKB:Q9STT2
Family Representative 		cargo adaptor activity
GO:0140312 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
retromer_vps35 Vps35 subfamilies
PANTHER:PTHR11099:SF0
Family 		cargo adaptor activity
GO:0140312 		Family Supported
Family review supports GO:0140312 FAMILY_WIDE. Vps35 is the conserved central platform of the retromer cargo-selective complex across Eukaryota (PTN000120819), directly associating with cytoplasmic tails of transmembrane cargos and with Vps26 and Vps29 to prevent lysosomal missorting.
retromer_vps35 Vps35 subfamilies
PANTHER:PTHR11099:SF6
Family 		cargo adaptor activity
GO:0140312 		Family Supported
Family review supports GO:0140312 FAMILY_WIDE. Vps35 is the conserved central platform of the retromer cargo-selective complex across Eukaryota (PTN000120819), directly associating with cytoplasmic tails of transmembrane cargos and with Vps26 and Vps29 to prevent lysosomal missorting.
retromer_vps35 Vps35 subfamilies
PANTHER:PTHR11099:SF5
Family 		cargo adaptor activity
GO:0140312 		Family Supported
Family review supports GO:0140312 FAMILY_WIDE. Vps35 is the conserved central platform of the retromer cargo-selective complex across Eukaryota (PTN000120819), directly associating with cytoplasmic tails of transmembrane cargos and with Vps26 and Vps29 to prevent lysosomal missorting.
retromer_vps29 Vps29 subfamily
PANTHER:PTHR11124:SF12
Family 		cargo adaptor activity
GO:0140312 		Family Supported
Family review supports GO:0140312 for PANTHER:PTHR11124:SF12. PAINT node PTN000122547 (taxon:2759, Eukaryota) places GO:0140312 (cargo adaptor activity) across eukaryotic Vps29 orthologs (PANTHER:PTHR11124:SF12), which scaffold the C-terminal arch of VPS35 in retromer and VPS35L in retriever; bacterial/archaeal members (PANTHER:PTHR11124:SF26) are soluble phosphodiesterases and do not form membrane-trafficking complexes.

Gene-review completeness (0/14 grounded genes reviewed)

0 complete review(s) · 0 with deep research · 14 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
VPS35C (Arabidopsis) A8R7K9 ✗ — —
VPS35B (Arabidopsis) F4I0P8 ✗ — —
VSR2 (Arabidopsis) O22925 ✗ — —
VSR5 (Arabidopsis) O64758 ✗ — —
VSR3 (Arabidopsis) O80977 ✗ — —
VSR1 (Arabidopsis) P93026 ✗ — —
BP80 (pea) P93484 ✗ — —
RMR1 (rice) Q69U49 ✗ — —
VPS35A (Arabidopsis) Q7X659 ✗ — —
VPS26A (Arabidopsis) Q9FJD0 ✗ — —
VSR6 (Arabidopsis) Q9FYH7 ✗ — —
RMR1 (Arabidopsis) Q9M622 ✗ — —
VPS29 (Arabidopsis) Q9STT2 ✗ — —
VPS26B (Arabidopsis) Q9T091 ✗ — —

Details

Context
ViridiplantaeNCBITaxon:33090
Vacuolar sorting receptor cycle in plantsBiological Processplant_vacuolar_sorting_receptor_cycle
protein targeting to vacuoleGO:0006623 retromer complexGO:0030904
Context
ViridiplantaeNCBITaxon:33090

Connections

vsr -> retromer Provides Input For
After cargo release, retromer retrieves the receptors for reuse.
Part 1: cargo recognition
Vacuolar sorting receptorMolecular Functionvsr

Annotons

Vacuolar sorting receptor (VSR)
vsr_receptor
Participant: Family: VSR subfamilies (UniProt and PANTHER-file placements)
Family:
VSR subfamilies (UniProt and PANTHER-file placements) UniProt and PANTHER's own files place the VSRs in different families, so the selector lists both. UniProt, the local entries table and GO's PAINT annotations use PTHR22702: SF1 (Arabidopsis VSR1-4 and pea BP80) and SF4 (VSR5-7); the cited node PTN008602288 (taxon:33090, Viridiplantae) places protein targeting to vacuole. PANTHER's release-19 Arabidopsis classification file instead places VSR1-6 in five plant-only subfamilies of the EGF-domain family PTHR24034 (SF166, SF199, SF171, SF180, SF181), which are also selected. PTHR24034:SF89 is excluded, because PANTHER's file places VSR7 there with animal CD93, so VSR7 is matched only through PTHR22702:SF4. PTHR22702:SF1 also holds the animal PRADC1 proteins in both sources, so outside plants this selector matches PRADC1, which is not a sorting receptor. The node carries no F IBD, so the step is left untyped. Descent is shown by the protein's IBA rows in QuickGO, which cite the node; no Arabidopsis gene review exists for it in this repository.
Representative Members: VSR1 (Arabidopsis)UniProtKB:P93026 VSR2 (Arabidopsis)UniProtKB:O22925 VSR3 (Arabidopsis)UniProtKB:O80977 VSR5 (Arabidopsis)UniProtKB:O64758 VSR6 (Arabidopsis)UniProtKB:Q9FYH7 BP80 (pea)UniProtKB:P93484

Locations

trans-Golgi networkGO:0005802

Type I membrane receptor that binds vacuolar sorting signals of soluble hydrolases at the trans-Golgi network and prevacuolar compartment and carries them toward the vacuole.

file:interpro/panther/PTHR22702/PTHR22702-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 1: cargo recognition (optional)
RMR storage-vacuole receptorMolecular Functionrmr

Optional: RMRs act on the storage-vacuole route, which not every plant cell or lineage uses, and their PAINT grounding is placed at rosids only.

Annotons

RMR receptor for storage-vacuole cargo
rmr_receptor
Participant: Family: RMR subfamily
Family:
RMR subfamilyPANTHER:PTHR47168:SF5 Subfamily PTHR47168:SF5 in UniProt and the local entries table, which lists Arabidopsis RMR1-6 and two rice RMRs. PANTHER's release-19 Arabidopsis classification file places Arabidopsis RMR1 in PTHR22765:SF334 instead; which placement is right has not been checked. PTN004566093 (taxon:71275, rosids) places intracellular protein transport; the family-level ubiquitin ligase node is not cited, so the step is left untyped. Descent is shown by the protein's IBA rows in QuickGO, which cite the node; no Arabidopsis gene review exists for it in this repository.
Representative Members: RMR1 (Arabidopsis)UniProtKB:Q9M622 RMR1 (rice)UniProtKB:Q69U49

Locations

trans-Golgi networkGO:0005802

RING-domain receptor proposed to sort storage proteins to protein storage vacuoles.

file:interpro/panther/PTHR47168/PTHR47168-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 2: receptor recycling
Retromer coreMolecular Functionretromer

Annotons

Retromer Vps35
retromer_vps35
Participant: Family: Vps35 subfamilies
Family:
Vps35 subfamilies Subfamilies PTHR11099:SF0 (VPS35A with the yeast, Dictyostelium and animal Vps35 proteins), SF6 (VPS35B) and SF5 (VPS35C). Descent is shown by the protein's IBA rows in QuickGO, which cite the node; no Arabidopsis gene review exists for it in this repository.
Representative Members: VPS35A (Arabidopsis)UniProtKB:Q7X659 VPS35B (Arabidopsis)UniProtKB:F4I0P8 VPS35C (Arabidopsis)UniProtKB:A8R7K9

Function

cargo adaptor activityGO:0140312 The F IBD at PTN000120819, placed at Eukaryota.

Locations

endosomeGO:0005768

Core retromer subunit that, with Vps26 and Vps29, retrieves sorting receptors from prevacuolar compartments for reuse.

GO_REF:0000033
PAINT IBD F:GO:0140312 at PTN000120819 in PTHR11099; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR11099/PTHR11099-paint.tsv
PAINT ancestral-node rows for this step's family.
Retromer Vps26
retromer_vps26
Participant: Family: Vps26 family
Family:
Vps26 familyPANTHER:PTHR12233 The whole family PTHR12233. Its plant subfamilies in PANTHER's release-19 Arabidopsis classification file (SF20, VPS26A; SF15, VPS26B) hold only Arabidopsis and poplar proteins in PANTHER's cached organism files, and every entry in the local entries table, plant or not, is listed without a subfamily, so a subfamily selector would fail most plant genomes for want of a placement. The family also holds VPS26C, a Commander-complex paralogue, so the step matches any Vps26 paralogue. PTN000260564 (Eukaryota) places retromer complex and carries no F IBD, so the step is left untyped. Descent is shown by the protein's IBA rows in QuickGO, which cite the node; no Arabidopsis gene review exists for it in this repository.
Representative Members: VPS26A (Arabidopsis)UniProtKB:Q9FJD0 VPS26B (Arabidopsis)UniProtKB:Q9T091

Locations

endosomeGO:0005768

Retromer subunit that binds Vps35 and cargo at the endosome.

file:interpro/panther/PTHR12233/PTHR12233-paint.tsv
PAINT ancestral-node rows for this step's family.
Retromer Vps29
retromer_vps29
Participant: Family: Vps29 subfamily
Family:
Vps29 subfamilyPANTHER:PTHR11124:SF12 Subfamily PTHR11124:SF12, from PANTHER's release-19 Arabidopsis classification file; the local entries table lists Arabidopsis VPS29 without a subfamily. In PANTHER's cached organism files the subfamily holds Vps29 of fungi, Dictyostelium and animals, and also the bacterial metallophosphoesterases Bacillus ysnB and Pseudomonas PA0351, so it does not separate retromer Vps29 outside eukaryotes. Descent is shown by the protein's IBA rows in QuickGO, which cite the node; no Arabidopsis gene review exists for it in this repository.
Representative Members: VPS29 (Arabidopsis)UniProtKB:Q9STT2

Function

cargo adaptor activityGO:0140312 The F IBD at PTN000122547, placed at Eukaryota.

Locations

endosomeGO:0005768

Retromer subunit that binds Vps35 and its regulators.

GO_REF:0000033
PAINT IBD F:GO:0140312 at PTN000122547 in PTHR11124; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR11124/PTHR11124-paint.tsv
PAINT ancestral-node rows for this step's family.