[001] Introduction

[002] Gadolinium is a key component of magnetic resonance imaging (MRI) contrast agents that are critical tools for enhanced detection and diagnosis of tissue and vascular abnormalities. Untargeted post-injection deposition of gadolinium in vivo, and association with diseases like nephrogenic systemic fibrosis (NSF), has alerted regulatory agencies to re-evaluate their wide spread use and generated calls for new, safer gadolinium-based contrast agents (GBCAs). Increasing anthropogenic gadolinium in surface water has also raised concerns of potential ecotoxicity and bioaccumulation in plants and animals. Methylotrophic bacteria can acquire, transport, store and use light lanthanides as part of a cofactor complex with pyrroloquinoline quinone (PQQ), an essential component of XoxF-type methanol dehydrogenases (MDHs). MDH catalyzes the oxidation of methanol to formaldehyde, a critical reaction for methylotrophic growth with methane and methanol.

[003] Summary of the Invention

[004] The invention provides microbial-based methods, compositions and systems for gadolinium recycling, using inexpensive growth substrates like methanol, with the option to produce the vitamin supplement pyrroloquinoline quinone (PQQ) as a value-added product. Practical applications of the invention include removal of gadolinium from medical waste and waste water; isolation of pure gadolinium (acquired from medical waste/waste water) to be reused for production of new MRI contrast agents; production of the vitamin PQQ. The invention also provides engineered bacteria for heavy lanthanide acquisition and storage.

[005] In an aspect the invention provides a method of removing a lanthanide from a medium, comprising growing a microbe in the medium under conditions wherein the growing microbe acquires the lanthanide from the medium, the microbe comprising a lanthanide-dependent alcohol dehydrogenase and an evo-MLn Methylorubrum extorquens AMI hybrid sensor histidine kinase/response regulator comprising a Leul51His substitution relative to the wild-type, GenBank: ACS39642.1; Ref Seq Accession WP_012752627.1.

[006] In embodiments:

[007] the medium comprises a growth substrate, such as methanol, ethanol or glycerol;

[008] the lanthanide is a heavy lanthanide, selected from gadolinium and europium (atomic numbers 64 and 63, respectively);

[009] the microbe is a Methylobacteriaceae species, including Methylobacterium species, such as Methylobacterium adhaesivum, Methylobacterium aminovorans, Methylobacterium aquaticum, Methylobacterium chloromethanicum, M. dichloromethanicum, Methylobacterium extorquens, Methylobacterium fujisawaense, Methylobacterium hispanicum, Methylobacterium isbiliense, Methylobacterium lusitanum, Methylobacterium mesophilicum, Methylobacterium nodularis, Methylobacterium organophilum, Methylobacterium podarium, Methylobacterium populi, Methylobacterium radiotolerans, Methylobacterium rhodesianum, Methylobacterium rhodinum, Methylobacterium suomiense, Methylobacterium thiocyanatum, Methylobacterium variabile, Methylobacterium zatmanii; and Methylorubrum species, such as Methylorubrum aminovorans, Methylorubrum extorquens, Methylorubrum podarium, Methylorubrum populi, Methylorubrum pseudosasae, Methylorubrum rhodesianum, Methylorubrum rhodinum, Methylorubrum salsuginis, Methylorubrum suomiense, Methylorubrum thiocyanatum and Methylorubrum zatmanii;

[010] the microbe is a Methylorubrum extorquens;

[Oil] the method further comprises, after acquisition of an amount of the lanthanide, isolating the microbe from the medium;

[012] the method further comprises isolating the lanthanide from the microbe;

[013] the microbe is grown under conditions wherein the microbe produces pyrroloquinoline quinone (PQQ);

[014] the microbe is grown under conditions wherein the microbe produces pyrroloquinoline quinone (PQQ), and the method further comprises isolating the PPQ from the microbe;

[015] the regulator is recombinant and/or transgenic to the microbe;

[016] the microbe is selected from an engineered Methylobacteriaceae species (supra) comprising a transgenic and/or recombinant regulator;

[017] the regulator is encoded by a regulator gene comprising 452T>A mutation that results in the Leul51His substitution; and/or

[018] the microbe comprises a genome comprising one or both of SNPs: 69T>C and 114T>C (GenBank: ACS39451.1; GenBank: ACS40444.1).

[019] In an aspect, the invention provides an engineered microbe for removing a lanthanide from a medium, the microbe comprising a lanthanide-dependent alcohol dehydrogenase and a transgenic and/or recombinant Methylorubrum extorquens AMI hybrid sensor histidine kinase/response regulator comprising a Leul51His substitution relative to the wild-type.

[020] In embodiments:

[021] the microbe is selected from an engineered Methylobacteriaceae species (supra);

[022] the microbe is a Methylorubrum extorquens; and/or

[023] the microbe comprises a genome comprising one or both of SNPs: 69T>C and 114T>C (GenBank: ACS39451.1; GenBank: ACS40444.1). [024] In an aspect the invention provides use of a disclosed microbe comprising a lanthanide- dependent alcohol dehydrogenase and an evo-HLn Methylorubrum extorquens AMI hybrid sensor histidine kinase/response regulator comprising a Leul51His substitution relative to the wild-type, GenBank: ACS39642.1; Ref Seq Accession WP_012752627.1, for the acquisition, storage and use of heavy lanthanides.

[025] The invention encompasses all combinations of the particular embodiments recited herein, as if each combination had been laboriously recited.

[026] Description of Particular Embodiments of the Invention

[027] Unless contraindicated or noted otherwise, in these descriptions and throughout this specification, the terms “a” and “an” mean one or more, the term “or” means and/or and polypeptide sequences are understood to encompass opposite strands as well as alternative backbones described herein. It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein, including citations therein, are hereby incorporated by reference in their entirety for all purposes.

[028] Physiological characterization of a Methylorubrum extorquens AMI genetic variant isolated from methanol growth with the heavy lanthanide gadolinium [029] ABSTRACT

[030] Here we report robust gadolinium-dependent methanol growth of a genetic variant of M. extorquens AMI, named evo-HLn, for “evolved for heavy lanthanides”. Genetic adaptation of evo-HLn resulted in the capability to grow on methanol using the heavy lanthanide gadolinium or europium, correlating with increased xoxl promoter and XoxF MDH activities, heavy lanthanide transport and storage, and increased biosynthesis of pyrroloquinoline quinone (PQQ). TVo-HLn was able to grow on methanol using the GBCA Gd-DTPA as the sole gadolinium source, showing the utility of this strain for gadolinium recovery from medical waste and/or wastewater and for generating new GBCAs.

[031] INTRODUCTION

[032] Gadolinium (Gd ³⁺ ; atomic number 64) is a versatile element that is widely used in various modem industries (1) but is perhaps best-known for its use as a contrast agent for MRI. Its seven unpaired electrons give Gd ³⁺ unparalleled paramagnetic properties, making it the most effective agent for clinical application (2). Gd ³⁺ alone is highly toxic to humans (3) and is therefore injected as a nine-coordinate ion chelated by an octadentate polyaminocarboxylate ligand with a water coligand (4). The stability of GBCAs makes them highly effective for intravenous delivery, and as a result they are used in an estimated 30 million MRI exams annually (5), with around half a billion doses administered thus far (6). GBCAs are excreted in urine post-injection, however, they are not innocuous. Over the past two decades, the development of NSF has been observed in GBCA injection patients with impaired renal function, resulting in joint pain, immobility and even death, (7-10). The last five years have generated rising alarm over the use of GBCAs with long-term retention found in the central nervous system, skin and bones of patients with normal kidney function (11-14). Anaphylactic shock and kidney failure have also been reported as possible outcomes of Gd ³⁺ accumulation in tissues (15, 16). Unmetabolized, excreted GBCAs are also cause for concern as rising anthropogenic Gd ³⁺ in surface water correlates with steadily increasing annual MRI exams worldwide (1). Due to the toxicity and rising concentrations of this microcontaminant, the potential health impacts on aquatic life and bioaccumulation in the food-chain deserve more attention, as do wastewater treatment strategies that are sufficient to remove Gd ³⁺ .

[033] Gadolinium is a member of the lanthanide series of elements, a group that has recently been added as life metals. A broader understanding of the functions of lanthanides (Ln ³⁺ ) in biology is slowly unfurling with discoveries of novel enzymes, metabolic pathways, and organisms dependent on these metals. Ln ³⁺ are known to form a cofactor complex with the prosthetic group PQQ for some alcohol dehydrogenase enzymes (17). XoxF MDH from the methylotrophic bacterium Methylorubrum (formerly Methylobacterium) extorquens AMI was the first reported Ln ³⁺ -dependent metallo-enzyme, and members of this diverse enzyme class are wide-spread in marine, fresh water, phyllosphere, and soil habitats (17-22). ExaF ethanol dehydrogenase was the first reported Ln ³⁺ -dependent enzyme with a preference for a multi carbon substrate, and its discovery has led to the identification of related enzymes in non- methylotrophic bacteria (23, 24). Ln ³⁺ are also known to influence metabolic pathways in methylotrophic and non- methylotrophic bacteria (25, 26). To date, all known Ln ³⁺ -dependent metallo-enzymes are from bacteria and coordinate the metal-PQQ complex for catalytic function. However, the physiological importance of PQQ stretches well-beyond the prokaryotes. Mammals, including humans (27), and plants (28) benefit from PQQ. Eukaryotes (29, 30) and archaea (31) produce PQQ-dependent enzymes, though there is still much to be discovered regarding their activities and function.

[034] Evidence for the biological use of lanthanides (Ln ³⁺ ) in bacteria was first reported as the stimulation of methanol growth and expression of PQQ-MDH activity in bacterial cultures grown with lanthanum (La ³⁺ ; atomic number 57) or cerium (Ce ³⁺ , atomic number 58) (32, 33). At the time, Ln ³⁺ were considered unavailable and unutilized for biological processes due to their insolubility in nature, and it was proposed that though Ln ³⁺ are more potent Lewis acids than calcium (Ca ²⁺ ), evolution likely passed them by in favor of the more bioavailable metal (34). PQQ-MDHs were typified by MxaFI, an α ₂ β ₂ tetrameric enzyme that coordinates Ca ²⁺ in the large subunit of each protomer (35, 36). MDH is a critical enzyme for methylotrophic bacteria, organisms that can oxidize reduced carbon compounds with no carbon-carbon bonds, such as methane and methanol, and has been the subject of genetic, biochemical and chemical studies for decades (37–42). Shortly after the discovery of Ln ³⁺ dependence for XoxF MDH activity in M. extorquens AM1 (18), the extremophile methanotroph Methylacidiphilum fumariolicum SolV was shown to rely on Ln ³⁺ in its volcanic mudpot environment for survival (43). Several subsequent studies noted the role of Ln ³⁺ in regulating MDH expression (44–46), describing the “lanthanide-switch” phenomenon in which the presence of light Ln ³⁺ up-regulates expression of xox genes and concomitantly down-regulates expression of mxa genes. Global studies have suggested that Ln ³⁺ may impact more than MDH and accessory gene expression, including alterations to downstream metabolism (25, 47, 48). [035] Growth studies with mesophilic methylotrophs and the Ln ³⁺ series of metals have shown that only members of the “light” classification, ranging from La ³⁺ to Nd ³⁺ (atomic number 60), can support growth with XoxF MDH similar to Ca ²⁺ with MxaFI MDH (49). In comparison, methanol growth with Sm ³⁺ is much slower and growth has not been reported for Ln ³⁺ of higher atomic numbers, with a couple of exceptions (20, 45, 50). M. fumariolicum SolV is able to grow with the light/heavy lanthanide Eu ³⁺ well enough to produce cultures for enzyme purification (51). This organism was also reported to show slow growth with Gd ³⁺ , but no studies have investigated this further (43). M. fumariolicum SolV grows optimally in acidic conditions (pH 2- 5) making Ln ³⁺ soluble for uptake and utilization, and as such does not have a known dedicated transport system for these metals. In contrast, methylotrophs that grow at neutral pH have an ABC transport system and specific TonB-dependent receptor encoded in a “lanthanide- utilization and transport” gene cluster (22, 52). Of such organisms known to date, only a genetically manipulated mutant strain of Methylotenera mobilis JLW8 has been reported to show positive signs of growth with Gd ³⁺ in the form of increased culture density (20). Thus, the heavy lanthanide Gd ³⁺ is the highest atomic number species known to support methanol growth in methylotrophic bacteria. Activity of XoxF MDH decreases with increasing atomic radius for the light Ln ³⁺ (25, 51). While decreasing XoxF MDH activity correlates with reduced growth rates seen with Ln ³⁺ of increasing atomic mass, it is still not known if this is due solely to decreased enzyme catalysis or if transport of the metal ions plays a role as well. Regardless of the factor(s) limiting growth, Gd ³⁺ seems to be the pivotal Ln ³⁺ marking the threshold of life with these metals. [036] Here we report the characterization of a M. extorquens AM1 genetic variant that is capable of robust growth on methanol with the heavy lanthanide Gd ³⁺ , a Ln ³⁺ that does not support growth in the ancestral strain. The variant has a single base-pair genetic change in a putative hybrid histidine kinase/response regulator that has no previously-known link with methylotrophy or Ln ³⁺ biochemistry. The variant exhibited increased xox1 promoter and MDH activities, a distinctive bright pink coloration corresponding to augmented PQQ production, and increased transport and storage of the metal. Further, genetic adaptation also allowed for faster growth with Sm ³⁺ and growth with the light/heavy lanthanide Eu ³⁺ . Finally, we show that the variant could grow efficiently with the GBCA Gd-DTPA as the sole Ln ³⁺ source. The invention provides methods and compositions for bioremediation and Ln ³⁺ recycling, and genetically- encoded and peptide-based imaging agents. [037] RESULTS [038] Isolation of an M. extorquens AM1 mutant strain capable of gadolinium-dependent methanol growth. The ΔmxaF mutant strain of M. extorquens AM1 has been reported to grow on methanol when provided an exogenous source of light lanthanides ranging from La ³⁺ to Sm ³⁺ , but heavy lanthanides such as Eu ³⁺ or Gd ³⁺ were not included in the study (45). Gadolinium is the heaviest Ln ³⁺ species that can be provided to produce a positive growth response (diminished growth compared to growth with light Ln ³⁺ ) in a methylotroph to date (49). To better understand the limit of Ln ³⁺ -dependent methanol growth of M. extorquens AM1, we first tested the ability of ΔmxaF to grow on methanol with Gd ³⁺ as the sole Ln ³⁺ available. MP methanol minimal medium with Gd ³⁺ was inoculated with ΔmxaF and culture density was measured over time. No detectable increase in culture density was observed after 14 days of incubation at 30°C. However, after another 7 days of incubation the culture density had increased ~2.3 fold, reaching a final OD ₆₀₀ of 0.35 ± 0.03 (N = 4). Gd ³⁺ -grown cells were transferred to fresh methanol minimal medium with Gd ³⁺ and grown to maximum culture density. This process was repeated twice. [039] To verify that the cultures were not contaminated, 5 μL was plated onto solid minimal succinate medium with 50 μg/mL rifamycin and incubated at 30°C. Growth of pink colonies indicated the cultures were M. extorquens AM1, as the strain used is rifamycin-resistant (53). Using colony PCR, we determined that cells recovered from the Gd ³⁺ -grown cultures were negative for mxaF, as was the ancestral strain, and positive for fae encoding formaldehyde- activating enzyme, another genetic marker specific for M. extorquens AM1. Cells from these Gd ³⁺ -grown cultures were washed four times with sterile minimal medium to remove possible residual extracellular Gd ³⁺ , resuspended in 1 mL sterile medium, and saved as freezer stocks with 5% DMSO at -80°C. [040] The long incubation time of the original cultures prior to growth with Gd ³⁺ suggested either an extended period of metabolic acclimation or genomic adaptation. To discern between these two possibilities, we tested methanol growth after first passaging the strain three times on solid succinate medium and then inoculating into liquid succinate medium to generate pre- cultures. Cells from the liquid culture were harvested, washed four times with sterile minimal medium, and then inoculated into methanol medium with Gd ³⁺ . Growth was measured using a microplate spectrophotometer. The variant strain exhibited growth within ~15 hours of inoculation, a specific growth rate of 0.03 ± 0.00 h ^-1 , and a maximum culture density 0.69 ± 0.04. The lack of the 3-week lag in growth, as we observed with the ancestral ΔmxaF inoculation, was indicative of genomic adaptation, rather than metabolic acclimation, being the underlying mechanism for growth with Gd ³⁺ . [041] Genomic DNA was isolated from the variant, sequenced, and analyzed for mutations relative to the wild type and ancestral ΔmxaF strains. Three single nucleotide polymorphisms (SNPs) were identified in the variant compared to ΔmxaF (Table S1). Only one of the three mutations was categorized as non-synonymous: a T to A nucleotide transition, resulting in a leucine to histidine amino acid substitution in a hybrid histidine kinase/response regulator. The mutation was confirmed by Sanger sequencing analysis, and the variant strain was named evo- HLn for “evolved for growth with heavy lanthanides”. [042] Increased PQQ biosynthesis. We observed that the cells of evo-HLn grown in methanol minimal medium with Gd ³⁺ had a distinctive, bright pink coloration, and that extracts prepared from evo-HLn cells retained this increased pigmentation. When analyzed by UV-visible spectrophotometry, evo-HLn extracts displayed a unique peak at 361 nm. A peak around this wavelength is a signature of PQQ when bound to XoxF MDH or ExaF EtDH (25, 54). To confirm PQQ was the cause of the absorption anomaly, we spiked it into the evo-HLn extracts and observed an increase at the same wavelength. After normalizing for protein concentrations, the absorbance spectra indicated PQQ in evo-HLn extracts was 4-fold higher compared to wild type and 6-fold higher compared to ΔmxaF extracts. [043] Expanded range of lanthanide utilization for methanol growth. Robust methanol growth dependent on the heavy lanthanide Gd ³⁺ was highly reproducible with evo-HLn, and we wondered if the acquired genetic adaptation(s) could impact the capacity for growth with other Ln ³⁺ . Compared to ancestral ΔmxaF, evo-HLn exhibited a statistically significant 22.9% slower growth rate on methanol with La ³⁺ (One-way analysis of variance (ANOVA) p < 0.001) (Table 1). This may be a result in a trade-off between the capacities to grow with light and heavy Ln ³⁺ . We also tested for increased utilization of Sm ³⁺ , the highest atomic number Ln ³⁺ shown to allow growth of ΔmxaF. Because it was reported that increasing the concentration of Sm ³⁺ ten times to 20 μM resulted in more robust growth of ΔmxaF (faster growth rate, higher growth yield (45)), we tested the impact of this concentration on methanol growth of evo-HLn with Sm ³⁺ . Compared to ΔmxaF, evo-HLn grew at nearly double the rate reaching a maximum culture density similar to cultures grown with La ³⁺ (Table 1). In addition, we tested for methanol growth of evo-HLn with the heavy lanthanides Eu ³⁺ and Dy ³⁺ . Unlike ΔmxaF, evo-HLn was able to grow with Eu ³⁺ , though the growth rate and yield were reduced compared to both Sm ³⁺ and Gd ³⁺ (Table 1). evo-HLn did not show appreciable growth with Dy ³⁺ . [044] Increased xox1 promoter and MDH activities. Since XoxF MDH is closely-linked with Ln ³⁺ -dependent methanol growth, one plausible explanation for the expanded range of metals used by evo-HLn was increased XoxF MDH activity. Reporter-fusion assays previously showed that xox1 promoter activity was stimulated by light Ln ³⁺ ranging from La ³⁺ to neodymium (atomic number 60), with only a minor increase above background activity with Sm ³⁺ (45). We measured xox1 promoter activity in evo-HLn with La ³⁺ and observed a 7-fold increase compared to ΔmxaF and an 11-fold increase compared to wild type. Next, we measured xox1 promoter activity with Gd ³⁺ from evo-HLn and observed a similar increase. Further, we did not detect xox1 promoter activity in wild type with Gd ³⁺ , showing that although the wild type grows with methanol in the presence of Gd ³⁺ , the regulatory switch from MxaFI MDH to XoxF MDH oxidation systems does not occur. This could be indicative of either the wild type being unable to transport Gd ³⁺ or Gd ³⁺ not functioning as a signal for the “lanthanide switch” in this strain. Regardless, it can be concluded that wild type grows on methanol using MxaFI MDH, the Ca ²⁺ /PQQ-dependent oxidation system, when Gd ³⁺ is present in the medium. [045] Next, we measured MDH activity in cell-free extracts of ΔmxaF and evo-HLn prepared from cultures grown with methanol and either La ³⁺ or Gd ³⁺ . When grown with La ³⁺ , MDH activity in evo-HLn extracts was ~3-fold higher than in ΔmxaF extracts, verifying increased production of XoxF enzyme. Ln ³⁺ species do not function equally well as part of the XoxF MDH cofactor complex, along with PQQ, and the enzyme active site is finely tuned for light Ln ³⁺ (49, 51). Therefore, a reduction in XoxF MDH function could be expected with Gd ³⁺ in the active site. MDH activity was detectable in extracts of evo-HLn grown with Gd ³⁺ corresponding to 68% of the activity measured in extracts of ΔmxaF with La ³⁺ . evo-HLn grows well with Gd ³⁺ , and increased production of XoxF MDH is likely a major contributor to this metabolic capability. Increased xox1 promoter and MDH activities of evo-HLn are indicative of increases in Ln ³⁺ transport and intracellular accumulation. [046] Enhanced Lanthanide accumulation in evo-HLn. Using inductively-coupled plasma optical emission spectroscopy (ICP-OES), we determined the Ln ³⁺ metal content of cells grown with methanol and a single Ln ³⁺ element species. We measured a significant (Student’s t-test, p < 0.05; n = 3) 57% increase in Gd ³⁺ from evo-HLn compared to La ³⁺ from ΔmxaF. This increase is striking, and to our knowledge, the first report of enhanced Ln ³⁺ uptake and intracellular storage in a methylotroph. [047] Efficient acquisition of Gd ³⁺ from the GBCA Gd-DTPA. Finally, the capacity of the evo-HLn strain to acquire Gd ³⁺ from the chelator diethylenetriamine pentaacetate (DTPA) was demonstrated. Despite the high stability of the Gd-DTPA complex (log K _therm 22, log K _cond 17; (55, 56)), evo-HLn was able to grow readily with no reduction growth rate compared to growth with soluble GdCl ₃ (Gd-DTPA, 0.04 h ^-1 ± 0.00; GdCl3, 0.03 h ^-1 ± 0.00; n = 3). This result indicates that evo-HLn has a highly effective means of sequestering Gd ³⁺ from DTPA, thus demonstrating a potential importance as a key player in Gd ³⁺ recycling and pollution remediation. [048] MATERIALS AND METHODS [049] Strains and culture conditions. M. extorquens AM1 strains were routinely grown at 30°C MP minimal medium (65) with 15 mM succinate, shaking at 200 rpm on an Innova 2300 platform shaker (Eppendorf, Hamburg, Germany). For growth studies, 50 mM methanol was used as the sole carbon and energy source. Lanthanides were added as chloride salts or gadopentetic acid (Gd-DTPA; Magnevist ^{®^} ) to a working concentration of 2 or 20 μM as indicated. When necessary, 50 μg/mL kanamycin was added to the growth medium for plasmid maintenance. Strains and plasmids used in this study are listed in Table S1 of the supplementary material. [050] Strain construction. M. extorquens AM1 strains were transformed by electroporation (66). After 24 hours of outgrowth transformants were selected by plating on MP medium with 1.5% agar, 15 mM succinate and 50 μg/mL kanamycin. Transformants grew for 72 hours at 30°C until individual colonies appeared. [051] Methanol growth analysis with light and heavy lanthanides. M. extorquens AM1 strains were grown with succinate overnight, cells were pelleted by centrifugation at 1,000 x g for 10 min at room temperature using a Sorvall Legend X1R centrifuge (Thermo Scientific, Waltham, MA, USA), and washed in 1 mL of sterile MP medium with methanol. For growth analysis in microplates, washed cells were resuspended in 200 μL of MP methanol medium and 10 μL were transferred to each microplate well with 0.64 μL MP methanol medium for inoculation. For growth studies with Gd-DTPA, 50 μL of inoculum was added to 3 mL MP methanol medium in sterile 14 mL polypropylene culture tubes (Fisher Scientific, Hampton, NH, USA). Cultures densities were monitored over time by measuring light scatter at 600 nm using either a Synergy HTX multi-mode plate reader (Biotek, Winooski, VT, USA) or an Ultraspec 10 density meter (Biochom, Holliston, MA, USA). [052] UV-visible spectrophotometry. To prepare cell-free extracts, 50 mL of methanol grown culture with Gd ³⁺ or La ³⁺ was harvested, upon reaching an OD^oo of -1.1-1.3, by centrifugation at 4,696 x g for 10 minutes at 4°C. The supernatant was removed and cell pellets were resuspended in 1.5 mL of 25 mM Tris, pH 8.0 and lysed using an OS Cell Disrupter at 25,000 psi (Constant Systems Limited, Low March, Daventry, Northants, United Kingdom). Lysates were transferred to 1.5 mL eppendorf tubes and clarified of cell debris by centrifugation at 21,000 x g for 10 minutes at 4°C. Cell-free extracts were transferred to new eppendorf tubes and kept on ice until needed. PQQ was prepared fresh to a working concentration of 5.3 mM in an opaque conical tube and kept on ice until needed. Absorbance spectra were measured from 250- 600 nm with a Synergy HTX multi-mode plate reader. A blank buffer spectrum was subtracted as background. Protein concentrations were determined by absorbance at 280 nm and the bicinchoninic acid assay (ThermoFisher Scientific, Waltham, MA, USA).

[053] Genomic DNA extraction and sequencing. The A mxaF and A mxaF_Gd mutant strains were grown in shake flasks with 50 mL MP with succinate to early exponential growth phase. Cultures were transferred to 50 mL conical tubes and cells were harvested by centrifugation using a Sorvall Legend XR1 centrifuge at 4,696 x g, 4 °C for 10 min. The supernatant was removed and the cell pellets were resuspended in 30 mL of TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) before transferring to a new conical tube. After adding 80 mg of lysozyme, samples were mixed by vortexing and then incubated at 37°C. Next, 1.6 mL of 10% sodium dodecyl sulfate and 1 mg proteinase K were added to the samples, vortexing after each addition, and then samples were incubated at 56°C for 16 hours. After, 4 mL of 5 M NaCl was added and samples were mixed by vortexing. Then, 4 mL of 2.2 mM hexadecyltrimethylammonium bromide with 5.6 mM NaCl pre-heated to 65 °C was added and samples were vortexed. Samples were split evenly between two 50 mL conical tubes and incubated for 10 minutes at 65°C. Next, 20 mL of p h en o 1 : c h 1 o ro I b rm : i s o a m y 1 alcohol (25:24:1) was added, samples were mixed by vortexing, and then spun at 4,696 x g for 10 minutes at room temperature. The aqueous phase was then transferred to a new conical tube and 20 mL chloroformdsoamyl alcohol (24:1) was added. Samples were mixed and spun at 4,696 x g for 10 minutes at room temperature, after which the aqueous phase was transferred to a clean conical tube. Isopropanol chilled at -20°C was then added to each sample at a ratio of 0.6: 1.0, samples were mixed and then incubated at - 20°C for 16 hours. Samples were then spun at 4,696 x g for 45 minutes at 4°C and the supernatant was removed. Pellets were washed with ice cold 70% ethanol and then spun at 4,696 x g for 5 minutes at 4°C. The supernatant was discarded and the pellets were dried at room temperature. DNA samples were then treated for RNA contamination by resuspending each pellet in 170 pL of DNase-free water, adding RNase I and incubating at 37°C for 1 hour. After 1 hour, 5 pL of each RNase I-treated and untreated sample were analyzed by gel-electrophoresis for trace RNA. After verifying that RNA was degraded, the RNase I was inactivated by heating the samples at 70°C for 15 minutes. Samples were then cooled on ice and 20 pL 3M sodium acetate and 550 pL 100% ethanol were added. After mixing, samples were incubated overnight at -20°C. DNA was pelleted by spinning the samples for 20 minutes at 21,000 x g and 4°C, after which the supernatant was carefully poured off. DNA pellets were washed with ice-cold 70% ethanol and then spun at 21,000 x g and 4°C for 5 minutes. Ethanol was removed by carefully pipetting and the DNA pellets were then air dried at room temperature. Finally, DNA samples were resuspended in 100 pL of DNase-free water. Samples were submitted to Genewiz (South Plainfield, NJ, USA) for whole genome sequencing using the Illumina HiSeq platform with 2 x 150 bp read length. Variant calling and analysis was performed by Genewiz.

[054] Transcriptional reporter fusion assays. Strains carrying VENUS yfp fusion constructs were grown on methanol in 48-well microplate format. Upon reaching a culture density of ODgoo -0.35, 200 pL of culture were transferred to an optical bottom black 96-well plate. Fluorescence was measured at an excitation wavelength of 485 nm and an emission wavelength of 520 nm. Relative fluorescence units (RFU) were calculated as raw fluorescence divided by OD^io- [055] Methanol dehydrogenase activity assays. Cell extracts were prepared as described above, but with an additional wash step in 20 mL of 100 mM Tris-HCl, pH 9.0 before lysing. Protein concentrations of cell-free extracts were determined by BCA assay. Methanol dehydrogenase activity was measured by monitoring the phenazine methosulfate (PMS)- mediated reduction of 2,6-dichlorophenol indophenol (DCPIP; aeoo _nm = 21 mM ^"1 cm ^"1 (25, 54, 67)) as described (45, 67-69). To reduce background activity, all assay reagents were dissolved in water; PES and DCPIP solutions were prepared in opaque tubes and kept on ice; and cell-free extracts were pre-incubated for 2 minutes at 30°C as recommended (70).

[056] Intracellular Ln ³⁺ quantification. After whole-cell MRI analysis, cell pellets were dehydrated at 65°C for 72 hours. Dried pellets were weighed before deconstruction in Aqua regia diluted in 2% nitric acid, and sonicated for 0.5 h before passing through 0.5 pm Whatman syringe filters. Metal contents were determined by ICP-OES using a Varian 710-ES ICP-OES (Santa Clara, CA, USA) with standard solutions purchased from Sigma- Aldrich.

[057] TABLE 1 Growth rates and yields of strains grown in minimal medium with methanol Ln ³⁺ . Culture density was monitored for up to 96 hours. strain Ln ³⁺ source' growth rate ⁹ growth yield ⁹ evo HLn DyCl ₃ n.d. e 2 μM LnCl ₃ provided as the sole source of Ln ³⁺ except where indicated

^# 20 μM LnCl ₃ provided as the sole source of Ln ³⁺

9 Values represent the averages of 10 biological replicates from 3 independent experiments except where indicated. Error bars are standard errors of the mean (SEM). n.d. is not determined. - is no growth.

^§ Values are the mean of 5 biological replicates from two independent experiments.

[058] TABLE SI. Bacterial strains and plasmids strain or plasmid description reference strains Methylorubrum extorquens AM1 wild type; rifamycin-resistant derivative (1) ΔmxaF deletion mutant (2) ΔmxaF deletion mutant variant adapted for methanol evo-HLn this study growth with heavy lanthanides plasmids P _L /O4/A1 expression vector with evo-HLn variant pNG326 ^r this study META1_1800 allele, Km pAP05 promoterless yfp fusion vector, Tc ^r (3) pES503 pAP05 with xox1 promoter region, Tc ^r (3) [059] TABLE S2. Mutations detected by genome resequencing of ΔmxaF and evo-HLn Wild-type M. extorquens AM1 was used as the reference strain for mapping. Green, mutations unique to ΔmxaF; yellow, mutations unique toevo-HLn. Chromo Region Type Ref Allele Cou Fre Qu locus_tag Coding Amino No some nt q al change acid n change CP0015 482893^4 In - C 47 100 200 META1p0458 - 10 82894 CP0015 1673173 SNV A G 110 100 200 META1p1592 69T>C No 10 CP0015 1873778 SNV T A 175 100 200 META1p1800 452T>A Leu151 Yes 10 His CP0015 2329711 Del G - 125 98 160 - 10 CP0015 2777457 SNV T G 38 97 160 META1p2648 408A>C No 10 CP0015 2803789 SNV C T 32 100 200 META1p2676 .63C>T No 10 CP0015 2803840 SNV T C 9 100 155 META1p2676 114T>C No 10 CP0015 2891642 SNV G C 185 100 200 METAlp2763 879C>G No

10

CP0015 3037769 Del C 190 95 200 METAlp2908 718delC Arg241f Yes

10 s

CP0015 3159071 Del G 94 97 160

10

CP0015 4001527.. Del CG - 122 85 200 META lp3891, 262_266 Ala88fs Yes

10 4001531 TG META lp3892 delGCA

C CG

CP0015 4322600 SNV G A 4 67 26 METAlp4234 960C>T NO

10

CP0015 580985 ^L 5 In C 128 98 200 META2p0619 468_469 Argl57f Yes

11 80986 insG s

CP0015 770863 Del G 52 95 160 META2p0816 890delG Ala298f Yes

11 s

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