NRAMP3.1

UniProt ID: B9NAE4
Organism: Populus trichocarpa
Review Status: DRAFT
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Gene Description

Trans-Golgi network NRAMP-family divalent metal transporter that can transport Mn and Fe in heterologous systems and has an in-planta role in cell-to-cell manganese distribution.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006879 intracellular iron ion homeostasis
IBA
GO_REF:0000033 		MARK AS OVER ANNOTATED
Summary: NRAMP3.1 can transport Fe in heterologous yeast assays, but the poplar/Arabidopsis complementation evidence does not support assigning the in-planta intracellular iron homeostasis role to this TGN-localized paralog.
Reason: The paper reports metal transport ability but also an inability to complement nramp3nramp4 phenotypes; GO:0006879 overstates the demonstrated in-planta function of NRAMP3.1.
Propagation Review
Root cause: PROPAGATION BAD
Failure modes: FUNCTIONAL DIVERGENCE
Sources checked:
CGD:CAL0000200710 SUPPORTS SOURCE BUT NOT TARGET
MGI:MGI:1345275 SUPPORTS SOURCE BUT NOT TARGET
MGI:MGI:1345279 SUPPORTS SOURCE BUT NOT TARGET
PANTHER:PTN000194431 SUPPORTS SOURCE BUT NOT TARGET
Donor NRAMPs support iron homeostasis in their own contexts, and the family-level review (interpro/panther/PTHR11706/PTHR11706-review.yaml, PTN000194431) finds the placement defensible for the transporter clades, NRAMP3.1's subfamily SF109 included -- its pruning applies only to the diverged EIN2 subfamily SF75. The flag here rests on target-specific counter-evidence: PtNRAMP3.1 failed to complement Arabidopsis nramp3nramp4, so the specific iron-homeostasis process claim does not carry over to this paralog.
SGD:S000004024 SUPPORTS SOURCE BUT NOT TARGET
UniProtKB:A0A2K1ZPK4 SUPPORTS SOURCE BUT NOT TARGET
UniProtKB:B9NAE4 SUPPORTS SOURCE BUT NOT TARGET
UniProtKB:P49279 SUPPORTS SOURCE BUT NOT TARGET
UniProtKB:P49281 SUPPORTS SOURCE BUT NOT TARGET
WB:WBGene00004876 SUPPORTS SOURCE BUT NOT TARGET
WB:WBGene00004877 SUPPORTS SOURCE BUT NOT TARGET
WB:WBGene00004878 SUPPORTS SOURCE BUT NOT TARGET
dictyBase:DDB_G0275815 SUPPORTS SOURCE BUT NOT TARGET
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
its inability to complement the nramp3nramp4 double mutant phenotypes
GO:0030026 intracellular manganese ion homeostasis
IBA
GO_REF:0000033 		ACCEPT
Summary: The manganese homeostasis annotation is supported by the poplar NRAMP3 functional study and is central to this paralog family.
Reason: Mn transport and altered Mn distribution are core NRAMP3 biology in poplar.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
Analysis of the function of this gene in transgenic poplars suggests that it has a novel function in the control of cell-to-cell transport of Mn.
GO:0005794 Golgi apparatus
IEA
GO_REF:0000044 		MODIFY
Summary: Golgi apparatus is correct but less specific than the experimentally shown trans-Golgi network membrane localization.
Reason: The more specific TGN membrane term captures both the compartment and membrane association.
Proposed replacements: trans-Golgi network membrane
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane.
PMID:35700212
the other copy has acquired a distinct localization to the Trans Golgi Network (TGN)
GO:0016020 membrane
IEA
GO_REF:0000002 		MODIFY
Summary: Generic membrane is correct but less informative than the experimentally supported organelle membrane localization.
Reason: The annotation should use the specific membrane compartment rather than the generic membrane parent.
Proposed replacements: trans-Golgi network membrane
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
Trans-Golgi network membrane localization is experimentally supported for NRAMP3.1.
PMID:35700212
the other copy has acquired a distinct localization to the Trans Golgi Network (TGN)
GO:0030001 metal ion transport
IEA
GO_REF:0000002 		MODIFY
Summary: Metal ion transport is correct but too broad for a characterized Mn/Fe NRAMP transporter.
Reason: Specific iron and manganese transmembrane transport terms better capture the experimentally supported activity.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability
GO:0046873 metal ion transmembrane transporter activity
IEA
GO_REF:0000002 		MODIFY
Summary: Metal ion transmembrane transporter activity is directionally correct but less specific than the demonstrated Mn and Fe transport activities.
Reason: Use the specific cation transporter activities supported by yeast complementation and UniProt curation.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
CATALYTIC ACTIVITY: Reaction=Mn(2+)(in) = Mn(2+)(out); Reaction=Fe(2+)(in) = Fe(2+)(out).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability
GO:0005384 manganese ion transmembrane transporter activity
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: This is the best existing molecular function annotation for the experimentally demonstrated Mn transport activity.
Reason: The term directly names the cation transport activity shown for this NRAMP protein.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
CATALYTIC ACTIVITY: Reaction=Mn(2+)(in) = Mn(2+)(out).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability
GO:0006826 iron ion transport
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: Iron ion transport is supported by experimental Fe transport evidence for this protein.
Reason: The biological process follows from direct Fe transmembrane transport by the NRAMP transporter.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
CATALYTIC ACTIVITY: Reaction=Fe(2+)(in) = Fe(2+)(out).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability
GO:0006879 intracellular iron ion homeostasis
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		MARK AS OVER ANNOTATED
Summary: NRAMP3.1 can transport Fe in heterologous yeast assays, but the poplar/Arabidopsis complementation evidence does not support assigning the in-planta intracellular iron homeostasis role to this TGN-localized paralog.
Reason: The paper reports metal transport ability but also an inability to complement nramp3nramp4 phenotypes; GO:0006879 overstates the demonstrated in-planta function of NRAMP3.1.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
its inability to complement the nramp3nramp4 double mutant phenotypes
GO:0030026 intracellular manganese ion homeostasis
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: The manganese homeostasis annotation is supported by the poplar NRAMP3 functional study and is central to this paralog family.
Reason: Mn transport and altered Mn distribution are core NRAMP3 biology in poplar.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
Analysis of the function of this gene in transgenic poplars suggests that it has a novel function in the control of cell-to-cell transport of Mn.
GO:0030026 intracellular manganese ion homeostasis
IMP
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: The manganese homeostasis annotation is supported by the poplar NRAMP3 functional study and is central to this paralog family.
Reason: Mn transport and altered Mn distribution are core NRAMP3 biology in poplar.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
FUNCTION: Can transport manganese (Mn) and iron (Fe).
PMID:35700212
Analysis of the function of this gene in transgenic poplars suggests that it has a novel function in the control of cell-to-cell transport of Mn.
GO:0032588 trans-Golgi network membrane
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: The trans-Golgi network membrane localization is experimentally supported for NRAMP3.1.
Reason: This term captures the localization that differentiates NRAMP3.1 from the vacuolar NRAMP3.2 paralog.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane.
PMID:35700212
the other copy has acquired a distinct localization to the Trans Golgi Network (TGN)
GO:0046873 metal ion transmembrane transporter activity
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		MODIFY
Summary: Metal ion transmembrane transporter activity is directionally correct but less specific than the demonstrated Mn and Fe transport activities.
Reason: Use the specific cation transporter activities supported by yeast complementation and UniProt curation.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
CATALYTIC ACTIVITY: Reaction=Mn(2+)(in) = Mn(2+)(out); Reaction=Fe(2+)(in) = Fe(2+)(out).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability
GO:0071421 manganese ion transmembrane transport
IDA
PMID:35700212
Duplication of NRAMP3 gene in poplars generated two homologo... 		ACCEPT
Summary: Manganese ion transmembrane transport is directly supported and is a core process for this NRAMP paralog.
Reason: The term is specific to the demonstrated Mn transmembrane transport process.
Supporting Evidence:
file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
CATALYTIC ACTIVITY: Reaction=Mn(2+)(in) = Mn(2+)(out).
PMID:35700212
both PotriNRAMP3.1 and PotriNRAMP3.2 have retained metal transport ability

Core Functions

Transports Mn(2+) at the trans-Golgi network membrane, with a core role in intracellular manganese homeostasis and cell-to-cell manganese distribution.

Molecular Function:
manganese ion transmembrane transporter activity
Directly Involved In:
manganese ion transmembrane transport intracellular manganese ion homeostasis
Cellular Locations:
trans-Golgi network membrane
Supporting Evidence:
  • file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
    FUNCTION: Divalent metal transporter. Can transport manganese (Mn) and iron (Fe).
  • file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt
    SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane.
  • PMID:35700212
    Analysis of the function of this gene in transgenic poplars suggests that it has a novel function in the control of cell-to-cell transport of Mn.

References

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Suggested Questions for Experts

Q: Which Populus tissues and developmental stages most depend on NRAMP3.1-mediated TGN manganese retrieval for leaf Mn distribution?

Q: Does NRAMP3.1 make any measurable contribution to Fe movement in planta, or is the Fe transport activity only detectable in heterologous assays?

Suggested Experiments

Experiment: Generate NRAMP3.1 loss-of-function poplar lines and map Mn and Fe distribution across vein and lamina tissues under Mn-replete and Mn-limited growth.

Type: targeted mutant physiology

📚 Additional Documentation

Notes

(NRAMP3.1-notes.md)

NRAMP3.1 notes

  • Reviewed existing GOA annotations against NRAMP3.1-uniprot.txt and GOA provenance.
  • Core interpretation: Trans-Golgi network NRAMP-family divalent metal transporter that transports manganese and iron and helps control cell-to-cell manganese movement in poplar.
  • Main evidence source: [file:POPTR/NRAMP3.1/NRAMP3.1-uniprot.txt].

  • Direct NRAMP paralog evidence: PMID:35700212.

  • Fe-homeostasis caveat: PMID:35700212 supports Fe transport in yeast but also notes its inability to complement the nramp3nramp4 double mutant phenotypes, so GO:0006879 is treated as over-annotated for NRAMP3.1 in planta.

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