Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph

Lanthanides (Ln) are the most recently described life metals and are central to methylotrophy (type of metabolism in which organic substrates without carbon-carbon bonds serve as carbon and energy source) in diverse taxa. We recently characterized a novel, Ln-dependent, and Ln-accumulating methylotroph, Beijerinckiaceae bacterium RH AL1, which requires lighter Ln (La, Ce, Nd) for methanol oxidation. Starting from two sets of incubations, one with different La concentrations (50 nM and 1 µM) and one with different Ln elements [La, Nd, or an Ln cocktail (containing Ce, Nd, Dy, Ho, Er, Yb)], we could show that La concentration and different Ln elements strongly affectaffectaffectgene expression and intracellular Ln accumulation. Differential gene expression analysis revealed that up to 41% of the encoded genes were differentially expressed. The effectseffectseffectsof La concentration and Ln elements were not limited to Ln-dependent methanol oxidation but reached into many aspects of metabolism. We observed that Ln influenceinfluenceinfluencethe flagellar and chemotactic machinery and that they affect polyhydroxyalkanoate biosynthesis. The most differentially expressed genes included lanM, coding for the well-characterized lanthanide-binding protein lanmodulin, and a glucose dehydrogenase gene linked to the conversion of β-D-glucose to D-glucono-1,5-lactone, a known potential metal chelator. Electron microscopy, together with RNAseq, suggested that Beijerinckiaceae bacterium RH AL1 can discriminate between Ln elements and that they are differently taken up and accumulated. The discrimination of Ln and links between Ln and various aspects of metabolism underline a broader physiological role for Ln in Beijerinckiaceae bacterium RH AL1.