Deep Learning Exploration Expands the Natural Diversity of Metallothioneins in the Archaea Domain

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Abstract
The diversity and functions of metallothioneins (MTs) in Archaea remain poorly understood. This study identifies 180 archaeal MTs from 406 genomes, revealing distinct evolutionary lineages and structural diversity. Phylogenetic analysis suggests a novel class with divergent ancestry. AlphaFold3-based modeling highlights conserved Cys-rich motifs and irregular structures, potentially enhancing adaptation to extreme environments. Functional assays show that four MTs (MT334126, MT382228, MT114104, and MT282443) increase cadmium resistance, while MT334126 and MT382228 also enhance copper resistance. Targeted mutations at key sites boost metal adsorption, validated by structural modeling. This work provides the first comprehensive insight into archaeal MTs, laying the foundation for environmental and biotechnological applications.
Funding Information
  • Natural Science Foundation of Hebei Province (B2024201049)
  • Science Research Project of Hebei Education Department (QN2024104)
  • The Excellent Youth Research Innovation Team of Hebei University (QNTD202401)
  • The Beijing-Tianjin-Hebei Basic Research Coâ??operation Program (25JJJJC0024)
  • The National Natural Science Foundation of China (32250015)
  • The National Natural Science Foundation of China (U21A2024)
  • Advanced Talents Incubation Program of the Hebei University (521100223211)

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