Biology subjects

Voutsinos, M. Y.

Publications and source records attributed to Voutsinos, M. Y..

4 recordsLinked to original sources

bioRxiv2026

Evidence for lanthanide and PQQ dependent dehydrogenases in Eukarya

Lanthanides function as enzyme cofactors in bacteria, where they are widely distributed in pyrroloquinoline quinone-dependent 8-bladed beta-propeller dehydrogenases. No lanthanide-dependent enzymes, however, have been described outside prokaryotes. Here, we combined structural bioinformatics, phylogenetics, AlphaFold3 co-folding, coordination-sphere comparison, and quantum-mechanical cluster modeling to search for and rank putative lanthanide-coordinating 8-bladed beta-propeller enzymes in Eukarya. We identified candidate lanthanide-coordinating proteins in a diverse range of eukaryotes, predominantly plants and fungi, including species of clear industrial and agricultural relevance. A high-confidence subset matched validated bacterial Ln-binders based on both geometric similarity to canonical Ln-binding sites and on predicted Ln3+ versus Ca2+ selectivity. Our findings indicate that lanthanide biology likely extends beyond bacteria, with implications for plant, fungal, and broader eukaryotic metabolism, and warrant targeted biochemical investigation.

bioinformatics↗

bioRxiv2026

Diverse and novel lanthanide-binding PQQ-dependent enzymes

First described pyrroloquinoline quinone-dependent (PQQ) eight-bladed {beta}-propeller proteins are calcium (Ca)-dependent, but many homologous bacterial enzymes are lanthanide (Ln)-dependent. Discovery of Ca-dependent six-bladed {beta}-propeller PQQ-dependent dehydrogenases motivated the search for Ln-dependent six-bladed {beta}-propeller PQQ-dependent enzymes in bacteria. Using in silico structural prediction of sequences from weathered rock, we identified [~]22,000 PQQ six-bladed {beta}-propeller proteins in bacteria from 77 phyla, of which 63% of sequences have the active site residues needed to bind Ln. PQQ and La binding was biochemically confirmed for enzymes from uncultivated Chloroflexi and Acidobacteria. In structural models, Ln-binding periplasmic proteins interact with TonB-dependent transporters that may enable Ln uptake. Most genomes also encode predicted Ln-and PQQ-dependent eight-bladed dehydrogenases that clade with diverse alcohol and sugar dehydrogenases. Thus, Ln-dependent six and eight-bladed PQQ-dependent {beta}-propeller proteins are implicated in diverse carbon substrate metabolisms in weathering rock and soil. We predict that many PQQ-dependent microbial enzymes are lanthanide dependent.

microbiology↗

bioRxiv2023

Extensive and diverse lanthanide-dependent metabolism in the ocean

Lanthanide (Ln)-dependent enzymes have evolved roles in organic carbon metabolism despite low Ln availability in natural environments1-8. The oceans are the major reservoir of dissolved organic carbon (DOC) on the planet, yet the prevalence and diversity of Ln-dependent enzymes in the ocean, and their biogeochemical importance in the ocean carbon cycle is unknown. Here, we analyzed a global ocean metagenomic/metatranscriptomic dataset and found Ln-dependent methanol-, ethanol- and putative sorbose- and glucose-dehydrogenases in all metagenomes and 20% of all resolved microbial genomes, with several individual organisms hosting dozens of unique Ln-dependent genes. We find that biological methanol oxidation in the ocean is overwhelmingly Ln-dependent, and that methanol dehydrogenases are the most highly expressed Ln-dependent genes in most ocean regions, particularly in surface oceans. As Ln availability is a function of phosphate concentration and pH, Ln-dependent metabolism likely underpins complex biogeochemical feedbacks determining the efficiency of organic matter remineralization, thus impacting the oceanic DOC pool and Earths climate system. The widespread biological utility of Ln also explains their nutrient-like vertical concentration profiles observed in ocean waters, and shows that the preferential utilization of light lanthanides by biology must be considered when interpreting patterns of relative Ln concentrations in seawater.

microbiology↗

bioRxiv2022

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for the release of phosphate to the biosphere, yet the microorganisms involved, and the genes required for lanthanide metabolism, are poorly understood. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilization and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found gene clusters implicated in lanthanide-based metabolism of methanol (primarily XoxF3 and XoxF5) are surprisingly common in microbial communities in moderately weathered granite where lanthanide phosphate minerals are dissolving. Notably, XoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria. The XoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied XoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilize lanthanide phosphates, it is notable that candidate siderophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. We conclude that the confluence in the zone of moderate weathering of phosphate mineral dissolution, lanthanide utilisation, and methanol oxidation (thus carbonic acid production) may be important during the conversion of granitic rock to soil.

microbiology↗