Rare-Earth RB-TnSeq Design

Why It Matters

The Atlas has metal fitness breadth but not rare-earth direct measurements. That makes rare-earth biology a high-value gap: the first experiment can be designed from existing cross-metal structure rather than starting from an arbitrary gene list.

Review Brief

What changed: the lanthanide methylotrophy claim adds genomic marker context, so this opportunity can now combine cross-metal inference with rare-earth marker calibration.

Why review matters: this is an experiment-design page. Reviewers should decide whether the candidate ranking and controls are strong enough to justify a concrete RB-TnSeq proposal.

Evidence to inspect:

• Lanthanide-dependent methylotrophy is widespread and soil-linked for marker context.
• Rare Earth Fitness Data Gap for the missing direct assay.
• Metal specificity versus general stress for controls.
• metal_specificity, counter_ion_effects, and Bakta/AlphaFold evidence for candidate selection.

Questions for reviewers:

• Which REE conditions and counter-ion controls are most important for a first experiment?
• Which taxa have both relevant biology and usable mutant libraries?
• Should xoxF/lanmodulin marker evidence shape organism choice, candidate genes, or both?
• What minimum result would move rare-earth inference from prediction to validation?

Evidence Base

The starting evidence is not a single hit table. It combines metal-specific fitness, counter-ion caveats, conserved family context, Bakta reannotation, AlphaFold structure, and field validation logic from BacDive. The opportunity is to turn that combined evidence into a defensible experimental design.

Work Package

Rank candidate families by metal specificity, conservation, annotation novelty, structural plausibility, and assay caveat load. Select organisms with strong library support and interpretable baseline metal phenotypes. Build controls that separate rare-earth effects from counter-ion, osmotic, and generic stress effects.

Decision Use

If this opportunity succeeds, rare-earth cross-metal inference can move from prediction to validation, and metal tolerance scores can record which candidates are supported by direct rare-earth assays.