Tonoplast proton pumping and solute transport in plants

The plant vacuole membrane, the tonoplast, carries two proton pumps, the V-ATPase and the pyrophosphate-energized H+-PPase, whose gradient drives the uptake of ions and metabolites by antiporters, while aquaporins and channels let water and ions move between the cytosol and the vacuole. This module is the green-lineage core of tonoplast transport beyond the V-ATPase, written so that it can be evaluated in a plant genome.

MODULE:plant_tonoplast_transportDRAFTCONCRETEBiological Processmodules/plant_tonoplast_transport.yaml
vacuolar transmembrane transportGO:0034486 plant-type vacuole membraneGO:0009705

Viridiplantae scope, with Arabidopsis representatives. Read as a satisfiability rule, a genome needs the vacuolar H+-pyrophosphatase, a TIP1 aquaporin and a vacuolar NHX exchanger; TPC1, TPK1, CLC-a and ALMT9 are optional. The V-ATPase is the separate eukaryote-wide rule vacuolar_atpase_acidification. AVP1 and ALMT9 take their subfamily from PANTHER's release-19 Arabidopsis classification file, because the local entries tables list them without one. The CLC-a selector lists Arabidopsis only, AVP1 lists Arabidopsis and poplar (in PANTHER's files) and the NHX selectors Arabidopsis and one rice protein, so other green lineages may fail for want of a selector; the TPK1 subfamily also holds animal K2P channels. Not modelled: the many other tonoplast transporters (sugar, metal, phosphate and organic-acid carriers) and the tonoplast calcium pumps and exchangers.

8Nodes
7Parts
0Variant Sets
0Variants
7Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:plant_tonoplast_transport 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) · 17 evidence or coverage gap(s) (17 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
avp1_pump AVP1 (Arabidopsis)
UniProtKB:P31414
Family Representative 		diphosphate hydrolysis-driven proton transmembrane transporter activity
GO:0009678 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nhx_exchanger NHX1 (Arabidopsis)
UniProtKB:Q68KI4
Family Representative 		potassium:proton antiporter activity
GO:0015386 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nhx_exchanger NHX2 (Arabidopsis)
UniProtKB:Q56XP4
Family Representative 		potassium:proton antiporter activity
GO:0015386 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nhx_exchanger NHX3 (Arabidopsis)
UniProtKB:Q84WG1
Family Representative 		potassium:proton antiporter activity
GO:0015386 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nhx_exchanger NHX4 (Arabidopsis)
UniProtKB:Q8S397
Family Representative 		potassium:proton antiporter activity
GO:0015386 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tip_aquaporin TIP1-1 (Arabidopsis)
UniProtKB:P25818
Family Representative 		water channel activity
GO:0015250 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tip_aquaporin TIP1-1 (rice)
UniProtKB:P50156
Family Representative 		water channel activity
GO:0015250 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tip_aquaporin TIP1-1 (maize)
UniProtKB:O64964
Family Representative 		water channel activity
GO:0015250 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tpk1_channel TPK1 (Arabidopsis)
UniProtKB:Q8LBL1
Family Representative 		outward rectifier potassium channel activity
GO:0015271 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tpk1_channel TPKA (rice)
UniProtKB:Q850M0
Family Representative 		outward rectifier potassium channel activity
GO:0015271 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
avp1_pump AVP1 (type I V-PPase) subfamily
PANTHER:PTHR31998:SF52
Family 		diphosphate hydrolysis-driven proton transmembrane transporter activity
GO:0009678 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31998:SF52.
nhx_exchanger Vacuolar NHX subfamilies
PANTHER:PTHR10110:SF163
Family 		potassium:proton antiporter activity
GO:0015386 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10110:SF163.
nhx_exchanger Vacuolar NHX subfamilies
PANTHER:PTHR10110:SF117
Family 		potassium:proton antiporter activity
GO:0015386 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10110:SF117.
nhx_exchanger Vacuolar NHX subfamilies
PANTHER:PTHR10110:SF159
Family 		potassium:proton antiporter activity
GO:0015386 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10110:SF159.
nhx_exchanger Vacuolar NHX subfamilies
PANTHER:PTHR10110:SF179
Family 		potassium:proton antiporter activity
GO:0015386 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10110:SF179.
tip_aquaporin TIP1 subfamily
PANTHER:PTHR45665:SF54
Family 		water channel activity
GO:0015250 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR45665:SF54.
tpk1_channel TPK1 subfamily
PANTHER:PTHR11003:SF291
Family 		outward rectifier potassium channel activity
GO:0015271 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11003:SF291.

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
TIP1-1 (maize) O64964 ✗ — —
TIP1-1 (Arabidopsis) P25818 ✗ — —
AVP1 (Arabidopsis) P31414 ✗ — —
TIP1-1 (rice) P50156 ✗ — —
CLC-A (Arabidopsis) P92941 ✗ — —
NHX2 (Arabidopsis) Q56XP4 ✗ — —
TPC1 (rice) Q5QM84 ✗ — —
NHX1 (Arabidopsis) Q68KI4 ✗ — —
NHX3 (Arabidopsis) Q84WG1 ✗ — —
TPKA (rice) Q850M0 ✗ — —
TPK1 (Arabidopsis) Q8LBL1 ✗ — —
NHX4 (Arabidopsis) Q8S397 ✗ — —
TPC1 (Arabidopsis) Q94KI8 ✗ — —
ALMT9 (Arabidopsis) Q9LS46 ✗ — —

Details

Context
ViridiplantaeNCBITaxon:33090
Tonoplast proton pumping and solute transport in plantsBiological Processplant_tonoplast_transport
vacuolar transmembrane transportGO:0034486 plant-type vacuole membraneGO:0009705
Context
ViridiplantaeNCBITaxon:33090

Connections

vppase -> nhx Provides Input For
The proton gradient drives NHX cation uptake.
vppase -> clca Provides Input For
The proton gradient drives CLC-a nitrate uptake.
Part 1: proton pumping
Vacuolar H+-pyrophosphataseMolecular Functionvppase

Annotons

Vacuolar H+-pyrophosphatase (AVP1)
avp1_pump
Participant: Family: AVP1 (type I V-PPase) subfamily
Family:
AVP1 (type I V-PPase) subfamilyPANTHER:PTHR31998:SF52 Subfamily PTHR31998:SF52, from PANTHER's release-19 Arabidopsis classification file; the local entries table lists Arabidopsis AVP1 without a subfamily. In PANTHER's cached organism files it holds Arabidopsis AVP1 and three poplar proteins; the bacterial H+-PPases and the Golgi-type AVP2 are in other subfamilies. 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: AVP1 (Arabidopsis)UniProtKB:P31414

Function

diphosphate hydrolysis-driven proton transmembrane transporter activityGO:0009678 The F IBD at PTN009132393.

Locations

plant-type vacuole membraneGO:0009705

Tonoplast proton pump that uses pyrophosphate hydrolysis to acidify the vacuole, alongside the V-ATPase.

GO_REF:0000033
PAINT IBD F:GO:0009678 at PTN009132393 in PTHR31998; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR31998/PTHR31998-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 2: proton-coupled ion uptake
Vacuolar NHX exchangerMolecular Functionnhx

Annotons

Vacuolar NHX Na+(K+)/H+ exchanger
nhx_exchanger
Participant: Family: Vacuolar NHX subfamilies
Family:
Vacuolar NHX subfamilies Subfamilies PTHR10110:SF163, SF117, SF159 and SF179, one for each of Arabidopsis NHX1-4; SF117 also lists rice NHX1. The plasma-membrane SOS1 and endosomal NHX5/6 exchangers are not selected. The cited F node is family-level and also places plasma membrane, so the tonoplast location is inferred from the subfamily, not the node. 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: NHX1 (Arabidopsis)UniProtKB:Q68KI4 NHX2 (Arabidopsis)UniProtKB:Q56XP4 NHX3 (Arabidopsis)UniProtKB:Q84WG1 NHX4 (Arabidopsis)UniProtKB:Q8S397

Function

potassium:proton antiporter activityGO:0015386 The potassium:proton antiporter F IBD at PTN008493947, a family-level node with no taxon, which also carries sodium:proton antiporter activity; the K+ term is used because the vacuolar NHX proteins load K+ as well as Na+ and the step's role covers both.

Locations

plant-type vacuole membraneGO:0009705

Tonoplast cation/proton antiporter that loads Na+ and K+ into the vacuole using the proton gradient.

GO_REF:0000033
PAINT IBD F:GO:0015386 at PTN008493947 in PTHR10110; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR10110/PTHR10110-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 2: proton-coupled ion uptake (optional)
CLC-a nitrate/proton antiporterMolecular Functionclca

Optional: this channel or transporter is a specialisation of particular cells and ions, and its distribution across Viridiplantae has not been checked here.

Annotons

CLC-a nitrate/proton antiporter
clca_antiporter
Participant: Family: CLC-a subfamily
Family:
CLC-a subfamilyPANTHER:PTHR11689:SF67 Subfamily PTHR11689:SF67, which lists Arabidopsis CLC-a only. The step is left untyped. The only F IBD on the cited nodes, at PTN000189597 (Magnoliopsida), is nitrate:proton symporter activity (GO:0009671), seeded by CLC-b (AT3G27170) rather than CLC-a; it is not used because this step describes an antiporter, so the symporter term conflicts with the step's own role. The node's nitrate transport P IBD is seeded by the CLC-a locus (AT5G40890). 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: CLC-A (Arabidopsis)UniProtKB:P92941

Locations

plant-type vacuole membraneGO:0009705

Tonoplast CLC antiporter that accumulates nitrate in the vacuole.

file:interpro/panther/PTHR11689/PTHR11689-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 3: water and ion channels
TIP1 aquaporinMolecular Functiontip

Annotons

Tonoplast intrinsic protein (TIP1)
tip_aquaporin
Participant: Family: TIP1 subfamily
Family:
TIP1 subfamilyPANTHER:PTHR45665:SF54 Subfamily PTHR45665:SF54, which lists TIP1 proteins of Arabidopsis, rice, maize and two Medicago species. TIP2 (SF9) is not selected, because PANTHER groups it with the animal AQP8 proteins. PTN005228575 places plant-type vacuole membrane. 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: TIP1-1 (Arabidopsis)UniProtKB:P25818 TIP1-1 (rice)UniProtKB:P50156 TIP1-1 (maize)UniProtKB:O64964

Function

water channel activityGO:0015250 The F IBD at PTN002318122, the aquaporin family node.

Locations

plant-type vacuole membraneGO:0009705

Tonoplast aquaporin that lets water cross the vacuolar membrane.

GO_REF:0000033
PAINT IBD F:GO:0015250 at PTN002318122 in PTHR45665; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR45665/PTHR45665-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 3: water and ion channels (optional)
TPC1 channelMolecular Functiontpc1

Optional: this channel or transporter is a specialisation of particular cells and ions, and its distribution across Viridiplantae has not been checked here.

Annotons

TPC1 slow vacuolar cation channel
tpc1_channel
Participant: Family: TPC1 subfamily
Family:
TPC1 subfamilyPANTHER:PTHR46988:SF2 Subfamily PTHR46988:SF2, which lists TPC1 of Arabidopsis, rice, barley, wheat and tobacco. PTN000799186 (taxon:3193, Embryophyta) places plant-type vacuole, vacuolar membrane and calcium transport and carries no F IBD, so the step is left untyped; the plant-type vacuole membrane location combines the node's two CC terms rather than being taken from it. 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: TPC1 (Arabidopsis)UniProtKB:Q94KI8 TPC1 (rice)UniProtKB:Q5QM84

Locations

plant-type vacuole membraneGO:0009705

Two-pore cation channel that forms the slow vacuolar current of the tonoplast.

file:interpro/panther/PTHR46988/PTHR46988-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 3: water and ion channels (optional)
TPK1 channelMolecular Functiontpk1

Optional: this channel or transporter is a specialisation of particular cells and ions, and its distribution across Viridiplantae has not been checked here.

Annotons

TPK1 tonoplast K+ channel
tpk1_channel
Participant: Family: TPK1 subfamily
Family:
TPK1 subfamilyPANTHER:PTHR11003:SF291 Subfamily PTHR11003:SF291, which lists Arabidopsis TPK1 and rice TPKa and also the animal K2P channels C. elegans sup-9 and Drosophila Task7, so outside plants it matches unrelated channels. 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: TPK1 (Arabidopsis)UniProtKB:Q8LBL1 TPKA (rice)UniProtKB:Q850M0

Function

outward rectifier potassium channel activityGO:0015271 The outward rectifier potassium channel F IBD at PTN000108561, the K2P family node placed at Eukaryota, whose seeds include the TPK1 locus (AT5G55630). The node also carries potassium ion leak channel activity, whose seeds do not include TPK1, so it is not used.

Locations

plant-type vacuole membraneGO:0009705

Two-pore K+ channel of the tonoplast.

GO_REF:0000033
PAINT IBD F:GO:0015271 at PTN000108561 in PTHR11003; no gene review for the Arabidopsis protein here.
file:interpro/panther/PTHR11003/PTHR11003-paint.tsv
PAINT ancestral-node rows for this step's family.
Part 3: water and ion channels (optional)
ALMT9 malate channelMolecular Functionalmt9

Optional: this channel or transporter is a specialisation of particular cells and ions, and its distribution across Viridiplantae has not been checked here.

Annotons

ALMT9 vacuolar malate channel
almt9_channel
Participant: Family: ALMT9 subfamily
Family:
ALMT9 subfamilyPANTHER:PTHR31086:SF90 Subfamily PTHR31086:SF90, from PANTHER's release-19 Arabidopsis classification file (Arabidopsis ALMT9 and one poplar protein); the local entries table lists ALMT9 without a subfamily. PTN001258125 (taxon:3193) places plant-type vacuole membrane 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: ALMT9 (Arabidopsis)UniProtKB:Q9LS46

Locations

plant-type vacuole membraneGO:0009705

Tonoplast anion channel that loads malate into the vacuole.

file:interpro/panther/PTHR31086/PTHR31086-paint.tsv
PAINT ancestral-node rows for this step's family.