Genomic Characterization of Rare Earth Binding byShewanella oneidensis

Abstract

Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO4685, a capsular polysaccharide (CPS) synthesis gene, disruption which results in an up to 79% increase in biosorption and nusA, a regulatory protein, disruption which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO3183 increase relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Taken together, these results begin to elucidate how various genes affect the membrane chemistry of S. oneidensis and offer potential targets for improving biosorption and separation of REE.

Constraints on Lanthanide Separation by Selective Biosorption

“…At each column step, the number of binding sites is adjusted to be equal to half of the total number of metal ions. Note that this decision is slightly different from the one we adopted in Medin et al 8 where the number of binding sites is adjusted so that half of all REE are biosorbed. Although these two options produce extremely similar results under the solution conditions and dissociation constants used in this article, they will diverge in when the REE concentration drops significantly below the dissociation constant.…”

“…As a result, we cannot perfectly predict the behavior of a repeated biosorption and elution process using the microbe. However, we can fit the preferences seen in our earlier work 8 to two useful models (a single-site and a triple-site model), and then calculate the future behavior as the solution is enriched. For these examples, we have chosen Eu as the target metal for purification as wild-type S. oneidensis has a preference for it under low ionic strength, high lanthanide concentration 8 .…”

“…We can then ask what happens in a separation process if we change the parameters of the models to predict the effect of the small selectivity changes conferred by single gene modifications 8 . Finally, we can ask what happens if we further change the parameters of the models to predict the effects of more extensive genomic editing.…”

“…To perform this fit, we used a minimization algorithm using the SCIPY package to fit two dissociation constants to the binding data for the wild-type S. oneidensis from our recent work 8 . This algorithm can be found in the FIT_FB_3S.PY in the REE-PURIFICATION repository 41 .…”

“…In a recent work, we characterized the genetics of lanthanide-biosorption by S. oneidensis. In total, we discovered 242 genes that control the overall level of REE-biosorption, and 10 that control REE-binding selectivity 8 . The functions of these genes range from synthesis of the lipopolysaccharide (LPS) layer on the outer membrane of S. oneidensis to assembly of mannose-sensitive hemagglutinin (MSHA) pilus.…”