{
  "map": "QBM-04",
  "title": "Iron-sulfur cluster biogenesis \u2014 ISC, SUF and CIA",
  "qbo_version": "0.1.0",
  "nodes": [
    {
      "node_id": "FE_SUPPLY",
      "qbo": "QBO:FE_SUPPLY",
      "label": "Cellular Fe / S supply",
      "kind": "simple_chemical",
      "compartment": "cytosol",
      "evidence_tier": "T2",
      "confidence": "verified",
      "quantum_class": [
        "structural_context"
      ],
      "nuclei": [],
      "agi": [],
      "magnetically_addressable": false,
      "rationale": "Note carefully what the cited work does and does not show. Islam 2020 and Vigani 2021 measured iron uptake and Fe-S interplay under altered field conditions \u2014 nutritional physiology. Neither measured cluster assembly. This entity is T2 because the field effect is demonstrated for the process it names; the assembly entities above remain T3 because that evidence does not reach them.\n",
      "caveat": null,
      "evidence": [
        {
          "ref": "Islam2020",
          "doi": "10.3389/fpls.2020.00325",
          "claim": "The geomagnetic field contributes to efficient iron uptake in Arabidopsis; reducing it to near-null affects root metal reductase activity.\n",
          "direction": "decrease",
          "field_regime": "NNMF",
          "species": "Arabidopsis thaliana"
        },
        {
          "ref": "Vigani2021",
          "doi": "10.3390/ijms221810166",
          "claim": "Geomagnetic-field-dependent modulation of iron-sulfur interplay in Arabidopsis, most pronounced under combined Fe and S deficiency.\n",
          "direction": "altered",
          "field_regime": "NNMF",
          "species": "Arabidopsis thaliana"
        },
        {
          "ref": "Narayana2018",
          "doi": "10.1016/j.lssr.2018.08.005",
          "claim": "Reduction of the geomagnetic field to near-null affects Arabidopsis root mineral nutrition.\n",
          "direction": "altered",
          "field_regime": "NNMF",
          "species": "Arabidopsis thaliana"
        }
      ]
    },
    {
      "node_id": "NFS1",
      "qbo": "QBO:NFS1",
      "label": "Cysteine desulfurase NFS1 (ISC)",
      "kind": "macromolecule",
      "compartment": "mitochondrial_matrix",
      "evidence_tier": "T4",
      "confidence": "inferred",
      "quantum_class": [
        "structural_context"
      ],
      "nuclei": [],
      "agi": [
        "AT5G65720"
      ],
      "magnetically_addressable": false,
      "rationale": null,
      "caveat": null,
      "evidence": []
    },
    {
      "node_id": "ISU1",
      "qbo": "QBO:ISU1",
      "label": "Scaffold ISU1 (ISC)",
      "kind": "macromolecule",
      "compartment": "mitochondrial_matrix",
      "evidence_tier": "T3",
      "confidence": "inferred",
      "quantum_class": [
        "iron_sulfur_2Fe2S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT4G22220"
      ],
      "magnetically_addressable": true,
      "rationale": "Holds a transient, solvent-exposed [2Fe-2S] cluster whose assembly involves iron redox chemistry and sulfide transfer. A nascent cluster on a scaffold is more exposed and shorter-lived than a mature one buried in a protein, which makes it a more credible point of perturbation than the finished product.\n",
      "caveat": "Entirely untested. No experiment has measured scaffold occupancy or transfer rate under any magnetic field condition.\n",
      "evidence": []
    },
    {
      "node_id": "FRATAXIN",
      "qbo": "QBO:FRATAXIN",
      "label": "Frataxin (FH)",
      "kind": "macromolecule",
      "compartment": "mitochondrial_matrix",
      "evidence_tier": "T4",
      "confidence": "verified",
      "quantum_class": [
        "structural_context"
      ],
      "nuclei": [],
      "agi": [
        "AT4G03240"
      ],
      "magnetically_addressable": false,
      "rationale": null,
      "caveat": null,
      "evidence": [
        {
          "ref": "Turowski2015",
          "doi": "10.1371/journal.pone.0141443",
          "claim": "Frataxin is localised to both chloroplast and mitochondrion and is involved in chloroplast Fe-S protein function in Arabidopsis.\n",
          "direction": "altered",
          "field_regime": null,
          "species": "Arabidopsis thaliana"
        }
      ]
    },
    {
      "node_id": "HSCB_GRXS15",
      "qbo": "QBO:HSCB_GRXS15",
      "label": "Transfer machinery (HSCB, GRXS15)",
      "kind": "complex",
      "compartment": "mitochondrial_matrix",
      "evidence_tier": "T3",
      "confidence": "inferred",
      "quantum_class": [
        "iron_sulfur_2Fe2S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT5G06410",
        "AT3G15660"
      ],
      "magnetically_addressable": true,
      "rationale": "GRXS15 binds a bridging [2Fe-2S] cluster in its dimeric form, so the cluster is genuinely in transit and solvent-accessible here rather than buried.\n",
      "caveat": null,
      "evidence": []
    },
    {
      "node_id": "NFU_CARRIERS",
      "qbo": "QBO:NFU_CARRIERS",
      "label": "NFU carriers (NFU4, NFU5)",
      "kind": "macromolecule",
      "compartment": "mitochondrial_matrix",
      "evidence_tier": "T3",
      "confidence": "inferred",
      "quantum_class": [
        "iron_sulfur_4Fe4S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT3G20970",
        "AT1G51390"
      ],
      "magnetically_addressable": true,
      "rationale": "Transiently hold clusters destined for aconitase, succinate dehydrogenase and lipoyl synthase \u2014 precisely the QBM-01/QBM-05 nodes the review nominates. If assembly were field-sensitive, this is the step that would show it first.\n",
      "caveat": null,
      "evidence": []
    },
    {
      "node_id": "ATM3_EXPORT",
      "qbo": "QBO:ATM3_EXPORT",
      "label": "ATM3 / ABCB25 sulfur export",
      "kind": "macromolecule",
      "compartment": "mitochondrial_inner_membrane",
      "evidence_tier": "T4",
      "confidence": "reported",
      "quantum_class": [
        "structural_context"
      ],
      "nuclei": [],
      "agi": [
        "AT5G58270"
      ],
      "magnetically_addressable": false,
      "rationale": null,
      "caveat": null,
      "evidence": [
        {
          "ref": "Lill2006",
          "doi": "10.1146/annurev.cellbio.22.010305.104538",
          "claim": "Cytosolic Fe/S protein biogenesis depends on export of a sulfur-containing intermediate from the mitochondrion.\n",
          "direction": "altered",
          "field_regime": null,
          "species": "multiple"
        }
      ]
    },
    {
      "node_id": "SUF_SYSTEM",
      "qbo": "QBO:SUF_SYSTEM",
      "label": "SUF system (plastid assembly)",
      "kind": "complex",
      "compartment": "chloroplast_stroma",
      "evidence_tier": "T3",
      "confidence": "inferred",
      "quantum_class": [
        "iron_sulfur_4Fe4S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT1G08490",
        "AT4G26500"
      ],
      "magnetically_addressable": true,
      "rationale": "Builds every cluster in the chloroplast, including PSI's FX/FA/FB and ferredoxin's [2Fe-2S]. It is the single upstream dependency of QBM-02's strongest nodes.\n",
      "caveat": null,
      "evidence": []
    },
    {
      "node_id": "CNFU_HCF101",
      "qbo": "QBO:CNFU_HCF101",
      "label": "Plastid cluster carriers (CnfU, HCF101)",
      "kind": "macromolecule",
      "compartment": "chloroplast_stroma",
      "evidence_tier": "T3",
      "confidence": "reported",
      "quantum_class": [
        "iron_sulfur_4Fe4S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT3G24430"
      ],
      "magnetically_addressable": true,
      "rationale": "The review names CnfU explicitly: Yabe et al. showed the chloroplastic NifU-like protein acts as a scaffold and is required for photosystem I biogenesis, which makes it the direct upstream dependency of QBO:PSI_FES.\n",
      "caveat": null,
      "evidence": [
        {
          "ref": "Yabe2004",
          "doi": "10.1105/tpc.020511",
          "claim": "The chloroplastic NifU-like protein CnfU can act as an Fe-S cluster scaffold and is required for biogenesis of ferredoxin and photosystem I.\n",
          "direction": "altered",
          "field_regime": null,
          "species": "Arabidopsis thaliana"
        }
      ]
    },
    {
      "node_id": "CIA_SYSTEM",
      "qbo": "QBO:CIA_SYSTEM",
      "label": "CIA system (cytosolic assembly)",
      "kind": "complex",
      "compartment": "cytosol",
      "evidence_tier": "T3",
      "confidence": "reported",
      "quantum_class": [
        "iron_sulfur_4Fe4S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT5G50960",
        "AT4G16440",
        "AT2G26060",
        "AT1G68310",
        "AT5G48120"
      ],
      "magnetically_addressable": true,
      "rationale": "The reason this map matters beyond bioenergetics: CIA clients include the enzymes of DNA replication and repair, so an assembly defect reaches genome maintenance, not just ATP supply.\n",
      "caveat": null,
      "evidence": []
    },
    {
      "node_id": "FES_CLIENTS",
      "qbo": "QBO:FES_CLIENTS",
      "label": "Fe/S client proteins",
      "kind": "complex",
      "compartment": "cell",
      "evidence_tier": "T3",
      "confidence": "inferred",
      "quantum_class": [
        "iron_sulfur_4Fe4S",
        "iron_sulfur_2Fe2S"
      ],
      "nuclei": [
        "57Fe",
        "33S"
      ],
      "agi": [
        "AT4G35830",
        "AT5G66760",
        "AT5G13430",
        "AT4G03280",
        "AT1G10960",
        "AT2G20860",
        "AT2G21790"
      ],
      "magnetically_addressable": true,
      "rationale": "Collected here so the map can show, in one edge, that a single assembly defect reaches respiration, photosynthesis, the TCA cycle, nitrogen and sulfur assimilation and DNA replication simultaneously. That breadth is the review's argument for why Fe/S biology deserves attention ahead of cryptochrome.\n",
      "caveat": null,
      "evidence": []
    }
  ]
}