Influence of lanthanides on (non-)methylotrophic metabolism in Beijerinckiaceae bacterium RH AL1

• Applicant: Dr. Carl-Eric Wegner
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms ; Microbial Ecology and Applied Microbiology
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 467713456

Rare earth elements (lanthanides) are exploited by humankind for numerous high-tech applications. A biological role for lanthanides was ruled out due to their low bioavailability, although it is known for years that lanthanide supplementation can have a positive effect on crops and livestock. The discovery of lanthanide-dependent enzymes in methylotrophic bacteria a few years ago was a reset for microbiology. The meanwhile known key role of lanthanides in methylotrophy makes them highly relevant with respect to microbial carbon cycling. Research in this field is limited as most work is done with few model organisms that do not reflect the taxonomic and anticipated functional diversity of microbes utilizing lanthanides. I want to use a new, lanthanide-dependent, methylotrophic isolate of the family Beijerinckiaceae, strain RH AL1, to gain a better mechanistic understanding about lanthanide-dependent metabolism. Distinct physiological and genomic features, such as the presence of multiple genes coding for lanthanide-dependent enzymes, make this strain especially suitable for studying lanthanide-dependent metabolism in a setting not limited to methylotrophy. I aim at understanding 1) the role of lanthanides in non-methylotrophic metabolism and its regulation, 2) how lanthanides are taken up, and 3) how lanthanide metabolism-related genes and gene products are distributed among prokaryotes. In order to tackle these questions, Beijerinckiaceae bacterium RH AL1 will be used to study gene expression changes under non-methylotrophic conditions using RNAseq. RNAseq will be combined with microfluidic droplet cultivation. The latter allows a high replication of cultivation and minuscule manipulations of cultivation conditions. In addition, I want to develop a genetic system in Beijerinckiaceae bacterium RH AL1 that allows us to carry out mutagenesis-driven screenings to identify gene products that are essential for lanthanide-dependent metabolism, especially uptake and shuttling, under methylotrophic and non-methylotrophic conditions. Cryo electron microscopy and proteomics shall be used to better understand intra- and extracellular lanthanide storage better. Starting from publicly available prokaryotic genome sequences and metagenomes, curated databases of genes linked to lanthanide utilization will be used to generate a biogeographic and taxonomic catalogue about genes coding for lanthanide-dependent proteins and where to find them. A deeper understanding of lanthanide-dependent metabolism opens up a multitude of avenues, including applications such as the biologically mediated recovery of these valuable metals coupled to the consumption of waste and inexpensive feedstocks such as methane and methanol.

• DFG Programme: Research Grants
• International Connection: USA
• Cooperation Partners: Dr. Joseph Cotruvo; Dr. N. Cecilia Martinez-Gomez; Dr. Elizabeth Skovran