Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Abstract

Author Contributions: V.C. designed and supervised the study. V.C. and L.P. performed the uranium exposure experiments and prepared the samples for proteomics. N.T., M.F. and L.F. performed microscopic analysis and ICP-AES measurements. B.A.-B. acquired the proteomics data and N.G., B.A.-B. and J.A. performed the proteomic analyses. P.O. and M.B. performed genomic and phylogenetic analyses and constructed ORF databases for proteomics. A.M.A. established UipA topology in vivo. N.G. purified the recombinant proteins and performed fluorescence titration experiments, assisted by N.B. N.G. and D.L. performed native mass spectrometry experiments. N.G. acquired FTIR data under C.B. supervision. N.G. prepared the samples for synchrotron-based analysis and participated in EXAFS data acquisition. C.D.A. performed EXAFS data acquisition and processing. N.B. and N.G. performed crystallization tests and obtained the protein crystals under supervision of P.A. P.A. and P.L. resolved the

A critical review of mineral–microbe interaction and co-evolution: mechanisms and applications

“…Specific strategies include biosorption of metals to biofilm, cell wall and extracellular polymeric substance (EPS); precipitation as minerals; redox reactions [e.g. Hg(II)→Hg(0)] [ 11 ]; and metal sequestration by binding to proteins/ligands [ 38 ]. Other mechanisms include expulsion of metals by permeability barrier, active efflux and suppression of influx [ 39 ].…”

Molecular Mechanisms Underlying Bacterial Uranium Resistance

“…Moreover, the C-terminal part of this single-pass transmembrane protein has a high uranyl binding affinity. The crystal structure of UipA displayed a tandem of PepSY domains in a swapped dimer with a negatively charged face, responsible for uranium binding ( Gallois et al, 2021 ). In addition, the production of carboxymethyl cellulose modified iron sulfide complex (CMC-FeS) by sulfate reducing bacteria was shown to have increased U(VI) removal capacity compared to chemically produced CMC-FeS because of the presence of extracellular polymeric substances (EPS) containing tryptophan and tyrosine residues ( He et al, 2021 ).…”

“…A negative regulator of stress-induced operons, ArsR ( Silver and Phung, 2005 ), seemed to be less abundant when uranium is internally biomineralized in M. oleivorans A9 but more abundant as long as uranium remains extracellularly ( Gallois et al, 2018 ). Interestingly, the TCS UipRS is located upstream the uranium binding protein UipA in multiple Microbacterium species, but a role in uranium sensing and resistance has not yet been shown ( Gallois et al, 2021 ). In D. alaskensis G20, a cyclic AMP receptor protein (CRP) was found to possibly regulate expression of the mre operon for metal reduction, facilitating uranium reduction through thioredoxin ( Li and Krumholz, 2009 ).…”

Optimized Coordination of Uranyl in Engineered Calmodulin Site 1 Provides a Subnanomolar Affinity for Uranyl and a Strong Uranyl versus Calcium Selectivity

“…Proteins as calmodulin site 1 or the Uranium Induced Protein A recently identified in a Microbacterium species resistant to uranium have uranyl binding sites with dissociation constants in the nanomolar range. 15,40 A subnanomolar (pH 6, K d = 200 pM) to femtomolar (pH 8.9, K d = 7.4 fM) affinity for uranyl was reported for an engineered protein. 12,36 In this protein, structural data at low pH proposed a uranyl equatorial coordination by two bidentate carboxylate groups and a water molecule and an additional electrostatic interaction between an arginine side-chain and one of the axial oxo groups of uranyl.…”

“…Importantly, not only phosphorylated sites can have a strong affinity for uranyl. Proteins as calmodulin site 1 or the Uranium Induced Protein A recently identified in a Microbacterium species resistant to uranium have uranyl binding sites with dissociation constants in the nanomolar range. , A subnanomolar (pH 6, K d = 200 pM) to femtomolar (pH 8.9, K d = 7.4 fM) affinity for uranyl was reported for an engineered protein. , In this protein, structural data at low pH proposed a uranyl equatorial coordination by two bidentate carboxylate groups and a water molecule and an additional electrostatic interaction between an arginine side-chain and one of the axial oxo groups of uranyl . The high affinity for uranyl of this protein lacking phosphoryl ligands raises the question of the role of the nature and structure of the first coordination sphere and of longer-range electrostatic interactions on the binding site affinity for uranyl.…”