A novel in-silico model explores LanM homologs among Hyphomicrobium spp.

Abstract

Investigating microorganisms in metal-enriched environments holds the potential to revolutionize the sustainable recovery of critical metals such as lanthanides (Ln³⁺). We observe Hyphomicrobium spp. as part of a Fe²⁺/Mn²⁺-oxidizing consortia native to the ferruginous bottom waters of a Ln³⁺-enriched lake in Czechia. Notably, one species shows similarities to recently discovered bacteria expressing proteins with picomolar Ln³⁺ affinity. This finding was substantiated by developing an in-silico ionic competition model and recombinant expression of a homolog protein (Hm-LanM) from Hyphomicrobium methylovorum. Biochemical assays validate Hm-LanM preference for lighter Ln³⁺ ions (from lanthanum to gadolinium). This is comparable to established prototypes. Bioinformatics analyses further uncover additional H. methylovorum metabolic biomolecules in genomic proximity to Hm-LanM analogously dependent on Ln³⁺, including an outer membrane receptor that binds Ln³⁺-chelating siderophores. These combined observations underscore the remarkable strategy of Hyphomicrobium spp. for thriving in relatively Ln³⁺ enriched zones of metal-polluted environments.