Rare Earth Element (REE)-Dependent Growth of Pseudomonas putida KT2440 Relies on the ABC-Transporter PedA1A2BC and Is Influenced by Iron Availability

Abstract

In the soil-dwelling organism Pseudomonas putida KT2440, the rare earth element (REE)-utilizing, and pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenase PedH is part of a periplasmic oxidation system that is vital for growth on various alcoholic volatiles. Production of PedH and its Ca2+-dependent counterpart PedE is inversely regulated in response to lanthanide (Ln3+) bioavailability, a mechanism termed the REE-switch. In the present study, we demonstrate that copper, zinc, and in particular, iron availability influences this regulation in a pyoverdine-independent manner by increasing the minimal Ln3+ concentration required for the REE-switch to occur by several orders of magnitude. A combined genetic and physiological approach reveals that an ABC-type transporter system encoded by the gene cluster pedA1A2BC is essential for efficient growth on 2-phenylethanol with low (nanomolar) Ln3+ concentrations. In the absence of pedA1A2BC, a ∼100-fold higher La3+-concentration is needed for PedH-dependent growth but not for the ability to repress growth based on PedE activity. From these results, we conclude that cytoplasmic uptake of lanthanides through PedA1A2BC is essential to facilitate REE-dependent growth on 2-phenylethanol under environmental conditions with poor REE bioavailability. Our data further suggest that the La3+/Fe2+/3+ ratio impacts the REE-switch through the mismetallation of putative La3+-binding proteins, such as the sensor histidine kinase PedS2, in the presence of high iron concentrations. As such, this study provides an example for the complexity of bacteria-metal interactions and highlights the importance of medium compositions when studying physiological traits in vitro in particular in regard to REE-dependent phenomena.

Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1

“…In Pseudomona putida KT2440, growth in the absence of the analogous Ln-ABC transporter still occurs if exogenous Ln 3+ concentrations are high (100 µM) and/or Fe 2+/3+ concentrations are low. These results suggest that in P. putida KT2440, Ln are in competition with metals such as Fe 3+ and can be transported by other metal (Fe 3+ ) transport systems when in excess 48 . Intriguingly, Gu and Semrau saw differential expression of multiple genes encoding ABC-type and TonB-dependent transporters in the methanotroph, Methylosinus trichosporium OB3b, when cerium was added to the growth medium 50 .…”

“…An analogous system in P. putida KT2440 exists where expression of the pedH and pedE genes, which encode Ln- and Ca-dependent ADHs respectively, are differentially regulated by Ln through the PedS2/R2 two-component system 10 . Unlike M. extorquens , Ln-ABC transport mutants of P. putida KT2440 express pedH when Ln are present, suggesting periplasmic Ln are enough to facilitate pedH expression 48 .…”

Do lanthanide-dependent microbial metabolisms drive the release of REEs from weathered granites?

“…To date, two transporters have been experimentally verified as required for lanthanide transport: the outer membrane siderophore-associated TonB-dependent transporter (Ochsner et al 2019) and the periplasmic ABC-type transporter (Wehrmann et al 2019). We identified two transport proteins not previously associated with XoxF systems, NRAMP and the mechanosensitive ion channel (MscS).…”

The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440

“…It further indicates that this regulatory system is functional under all tested conditions. The only other two proteins (PedH and PP_2673) that showed differential abundance under more than one set of culture conditions are encoded by genes within the ped gene cluster, which encodes several crucial elements for regulation and function of PedE and PedH (13,43,47). Notably, the carbon sources provided under the conditions in which these proteins were identified either represent substrates of PedE and PedH (2-phenylethanol and glycerol) or can be converted by an enzyme depending on the same PQQ cofactor, namely, the glucose dehydrogenase Gcd (glucose).…”

“…The aforementioned observations suggest that apart from the inverse transcriptional regulation of PQQ-ADHs, which has been described in detail for different organisms, including P. putida (12,13,20,28,(39)(40)(41)(42)(43), additional cellular responses to REEs exist and could depend on the specific organism and/or environmental context. To investigate the existence of such conditional responses in the nonmethylotrophic organism P. putida KT2440, we used a differential proteomic approach during growth on various model carbon sources that reflect the metabolic diversity of the rhizosphere.…”