Rare Earth Element (REE) Extraction Pathways (Biological Systems)

SCOPING BIOLOGY_DOMAIN

Species: METEA

Genes: mluA mluR mluI mllA mllBC mllDE mllF mllG mllH mllJ lanM xoxF1 xoxG xoxJ pqqA pqqE

Rare Earth Element (REE) Extraction Pathways (Biological Systems)

Bottom line: rare earth elements are recovered today by mineral processing
that is chemically harsh and poorly selective, while some bacteria already
solubilize, import and store lanthanides as part of normal metabolism. This
page is a design document for an engineered biological pipeline built from four
modules: metal sensing and controlled leaching, selective binding and uptake,
intracellular sequestration, and triggered export into a recovery solution. It
maps concrete Methylorubrum extorquens AM1 loci for the mll lanthanophore
cluster, the mlu cell-surface signaling cluster, lanM, the
xoxF/xoxG/xoxJ methanol dehydrogenase module, and pqq cofactor
biosynthesis, and it keeps the czc/cnr/rcnA efflux systems, smtA, and
ppk as non-METEA engineering candidates still to choose. It is scoped, not
started: no experiments, no curation batch for the non-METEA modules, and the
storage and export loci in AM1 are explicitly unmapped
(#3973). Related
gene reviews for the AM1 mll, mlu, lanM, xox and pqq genes live
under genes/METEA/; the lanthanophore subset is tracked by the
METEA_MLL_CLUSTER project.

The chassis comparison is the practical output so far: AM1 wins on REE
selectivity and loses on acid tolerance, which is why the blueprint separates
leaching from uptake rather than asking one organism to do both.

Scope

Targeted metal classes:

System goals:

  1. Detect metal ions in complex matrices
  2. Mobilize metals via leaching (acidolysis, redoxolysis)
  3. Bind and sequester selectively
  4. Concentrate intracellularly
  5. Trigger controlled export into recovery solution

Candidate Chassis (Starting Points)

Chassis Focus: Methylorubrum extorquens AM1 (METEA)

Mapping below uses locus tags from the METEA gene set. Locus tag format: MexAM1_META1p####.
See METEA-specific notes: METEA_MLL_CLUSTER.md.

High-Level Pipeline (Conceptual)

[Insoluble minerals/adsorbents]
          |
          |  (biosensor-triggered leaching)
          v
   [Solubilized metal ions]
          |
          |  (selective binding + uptake)
          v
   [Intracellular sequestration]
          |
          |  (storage/concentration)
          v
   [Inducible export/release]
          |
          v
   [Recovery solution: high-purity metal fractions]

Module 1: Adaptive Biosensors + Leaching Control

Objective: Sense target metal ions and induce production of leaching agents to solubilize metals through acidolysis and redoxolysis.

Design elements:

Leaching agent classes:

Example control logic:

IF (REE_high OR Co_high) AND (pH_buffer_ok) THEN
  upregulate acidolysis + redoxolysis modules
ELSE
  maintain basal leaching

Control logic (diagram):

flowchart TD A[REE/Co/Ni/Mn signals] --> B[Metal sensor TFs / riboswitches] C[pH buffer status] --> D{Logic gate} B --> D D -->|TRUE| E[Activate mll/mlu genes
META1p4129-4138] D -->|FALSE| F[Basal leaching] E --> G[Methylolanthanin secretion] G --> H[Solubilized ions]

Candidate chassis:

Gene system candidates (examples to validate in chassis):

M. extorquens AM1 locus map (lanthanophore-driven mobilization):

M. extorquens AM1 PQQ cofactor loci for XoxF/Mxa methanol dehydrogenases:

Module 2: Selective Binding + Uptake

Objective: Capture solubilized metals with high selectivity and transfer them into the cell.

Key components:

Selectivity strategies:

Control logic (diagram):

flowchart TD A[Solubilized REE/Co/Ni/Mn] --> B[Surface/Periplasmic binders] B --> C{Selectivity gate} C -->|REE favored| D[Lut cluster uptake
META1p1778-1787] C -->|Competing metals| E[Reject/low uptake] D --> F[Intracellular pool + lanM
META1p1786] F --> G[XoxF1 MDH utilization
META1p1740-1742]

Candidate chassis:

Gene system candidates (examples to validate in chassis):

M. extorquens AM1 locus map (lanthanide uptake):

Module 3: Intracellular Sequestration + Concentration

Objective: Store metals safely and concentrate to useful levels.

Storage strategies:

Potential readouts:

Control logic (diagram):

flowchart TD A[Intracellular REE] --> B[Sequestration modules] B --> C[PolyP/lanthasome-like storage
(METEA loci TBD)] C --> D[Storage granules] D --> E[Concentration readout]

Candidate chassis:

Gene system candidates (examples to validate in chassis):

M. extorquens AM1 locus map (storage):

Module 4: Inducible Export + Recovery

Objective: Release concentrated metals into recovery solutions after biomass harvest.

Trigger options:

Purity strategies:

Example timing sequence:

T0: Harvest biomass
T1: Induce REE export (selective efflux)
T2: Wash + collect REE fraction
T3: Induce Co/Ni/Mn export (secondary fraction)

Control logic (diagram):

flowchart TD A[Post-harvest trigger] --> B{Release mode} B -->|Efflux| C[Export pumps (METEA loci TBD)] B -->|Lysis| D[Controlled lysis] B -->|Chelator| E[Exchange release] C --> F[REE fraction] D --> F E --> F F --> G[Recovery solution]

Candidate chassis:

Gene system candidates (examples to validate in chassis):

M. extorquens AM1 locus map (export):

Integrated Pathway Blueprint (Simplified)

   Metal sensing
        |
        v
[TF/Riboswitch]---(logic)---->[Leaching agents]
        |                          |
        |                          v
        |                    [Solubilized ions]
        |                          |
        v                          v
[Selective binding] ---> [Uptake transporters]
        |
        v
[Sequestration + storage]
        |
        v
[Inducible export]
        |
        v
[Recovery solutions]

Engineering Considerations

Chassis Comparison (Decision Aid)

Chassis Strengths Primary role in REE pipeline Key tradeoffs Best-fit module(s)
Methylorubrum extorquens AM1 (METEA) Native lanthanide utilization; lanthanophore + lut uptake + xoxF High-selectivity REE acquisition and intracellular handling Sensitive to harsh acid leaching; export loci still TBD Binding/uptake, sequestration
Acidithiobacillus ferrooxidans Extreme acid tolerance; Fe(II) oxidation Aggressive bioleaching via acidolysis/redoxolysis Limited genetic toolset; growth conditions specialized Biosensor/leaching
Cupriavidus/Ralstonia sp. CH34 Broad metal resistance; czc/cnr efflux Post-harvest export/fractionation and detox Lower REE specificity; needs engineered uptake Export/recovery
Pseudomonas chlororaphis Robust secretion; phenazine redox shuttles Redox-assisted leaching + possible siderophore support REE selectivity weak; biosensor tuning needed Leaching

Decision criteria (pick one axis to optimize):

Scoring Rubric (3-Axis)

Scales: 1 (low) to 5 (high). Weights (default): REE selectivity 0.45, leaching strength 0.35, metal tolerance 0.20.

Chassis REE selectivity Leaching strength Metal tolerance Weighted score
Methylorubrum extorquens AM1 (METEA) 5 2 3 3.75
Acidithiobacillus ferrooxidans 1 5 5 3.00
Cupriavidus/Ralstonia sp. CH34 2 2 5 2.75
Pseudomonas chlororaphis 2 4 3 2.85

Notes:

Experimental Milestones

  1. Build metal-responsive reporter strains for REE/Co/Ni/Mn
  2. Validate leaching agent induction in mineral matrices
  3. Measure selective uptake vs. competing metals
  4. Demonstrate intracellular concentration without growth collapse
  5. Trigger export and quantify metal purity in recovery solutions

References (Starting Points)

Open Questions

Next Steps