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

Abstract

Lanthanides are the most recently described life metals and are central to methylotrophy in diverse taxa. We recently characterized a novel, lanthanide-dependent, and lanthanide-accumulating methylotroph, Beijerinckiaceae bacterium RH AL1, that utilizes lighter lanthanides (La, Ce, Nd) for methanol oxidation. We show that lanthanum concentration and different lanthanide (Ln) elements strongly affect gene expression and intracellular lanthanide accumulation. Differential gene expression analysis based on incubations with either La (50 nM or 1 µM), Nd (1 µM), or a lanthanide cocktail ([La, Ce, Nd, Dy, Ho, Er, Yb], equimolarly pooled, 1 µM), revealed that up to 41% of the encoded genes were differentially expressed. The effects of lanthanum concentration and Ln elements were not limited to lanthanide-dependent methanol oxidation but reached into many aspects of metabolism. We observed that lanthanides control the flagellar and chemotactic machinery and that they affect polyhydroxyalkanoate (PHA) biosynthesis. Secretion and various uptake systems, and carbohydrate metabolism were highly responsive. The most differentially expressed genes encode various unknown or hypothetical proteins, but alsolanM, coding for the well-characterized lanthanide-binding protein lanmodulin, and a glucose dehydrogenase gene linked to the conversion of β-D-glucose to gluconolactone, a known metal chelator. Electron microscopy, together with RNAseq, suggested different and potentially selective mechanisms for the uptake and accumulation of individual Ln elements. Mechanisms for discriminating lanthanides and links between lanthanides and various aspects of metabolism underline a broader functional role for lanthanides, possibly by functioning as calcium complements or antagonists.ImportanceSince its discovery, lanthanide-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding lanthanide recycling and circular economy. The physiological role of lanthanides is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) lanthanides affect metabolism have rarely been done. Our research shows that strain RH AL1 distinguishes different lanthanide elements and that the effect of lanthanides reaches into many aspects of physiology, for instance, motility and polyhydroxyalkanoate metabolism. Numerous differentially expressed genes coding for unknown or hypothetical proteins might hide so far unknown lanthanide-binding proteins. Our findings regarding lanthanide accumulation suggest different mechanisms for dealing with individual lanthanide elements and provide insights relating to intracellular lanthanide homeostasis. Understanding comprehensively how microbes distinguish and handle different lanthanide elements is key for turning knowledge into application regarding lanthanide-centered biometallurgy.

Changes in growth, lanthanide binding, and gene expression inPseudomonas alloputidaKT2440 in response to light and heavy lanthanides

“…We could show that Ln have a tremendous effect on gene expression in Beijerinckiaceae bacterium RH AL1, which does not possess Ca-dependent PQQ ADH and lacks the Ln switch. Up to 41% of the encoded genes were differentially expressed in strain RH AL1 dependent on Ln supplementation (45).…”

“…Transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy (EDX) analyses were done as described previously (37, 45).…”

“…It is not clear how Ln-utilizing microbes distinguish between them. Using Beijerinckiaceae bacterium RH AL1, we could show that Ln are selectively taken up and that supplementation with different Ln elements had only minor effects on growth but substantial effects on gene expression (20).…”

“…We could show that Ln have a tremendous effect on gene expression in Beijerinckiaceae bacterium RH AL1, which does not possess Cadependent PQQ ADH and lacks the Ln switch. Up to 41% of the encoded genes were differentially expressed in strain RH AL1 dependent on Ln supplementation(45).proteins were among the most differentially expressed genes dependent on Ln supplementation. This family of proteins of unknown function is conserved within the Pseudomonadaceae.…”

Impact of a Biological Chelator, Lanmodulin, on Minor Actinide Aqueous Speciation and Transport in the Environment

“…Despite LanM appearing to be nonessential under laboratory conditions for lanthanide uptake and lanthanide-dependent growth in M. extorquens, LanM proteins in several bacteria are among the most upregulated in response to the presence of lanthanides, − and later work has identified phenotypes associated with LanM deletion that point to a role in Ln uptake and homeostasis . The characterized LanMs display a diversity of mechanisms to discriminate between light and heavy lanthanides, ,, including metal-sensitive dimerization, but share to-date unmatched, high affinity and selectivity for trivalent lanthanides and actinides.…”