The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440

Wehrmann, Matthias; Berthelot, Charlotte; Billard, Patrick; Klebensberger, Janosch

doi:10.1128/msphere.00376-18

Cited by 33 publications

(29 citation statements)

References 52 publications

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“…Therefore, MxbD is necessary for mxaF expression but not for xoxF1 (Figure 4). Similar suppression mutants have been isolated from M. extorquens strain PA1 [30] and P. putida KT2440 [55]. The mutations found in the HAMP domain may confer signaling to the intracellular domain in the absence of ligand binding [56,57].…”

Section: The Mutation In Mxbd De-repress Mxafsupporting

confidence: 59%

Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A

et al. 2020

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Lanthanides (Ln) are an essential cofactor for XoxF-type methanol dehydrogenases (MDHs) in Gram-negative methylotrophs. The Ln3+ dependency of XoxF has expanded knowledge and raised new questions in methylotrophy, including the differences in characteristics of XoxF-type MDHs, their regulation, and the methylotrophic metabolism including formaldehyde oxidation. In this study, we genetically identified one set of Ln3+- and Ca2+-dependent MDHs (XoxF1 and MxaFI), that are involved in methylotrophy, and an ExaF-type Ln3+-dependent ethanol dehydrogenase, among six MDH-like genes in Methylobacterium aquaticum strain 22A. We also identified the causative mutations in MxbD, a sensor kinase necessary for mxaF expression and xoxF1 repression, for suppressive phenotypes in xoxF1 mutants defective in methanol growth even in the absence of Ln3+. Furthermore, we examined the phenotypes of a series of formaldehyde oxidation-pathway mutants (fae1, fae2, mch in the tetrahydromethanopterin (H4MPT) pathway and hgd in the glutathione-dependent formaldehyde dehydrogenase (GSH) pathway). We found that MxaF produces formaldehyde to a toxic level in the absence of the formaldehyde oxidation pathways and that either XoxF1 or ExaF can oxidize formaldehyde to alleviate formaldehyde toxicity in vivo. Furthermore, the GSH pathway has a supportive role for the net formaldehyde oxidation in addition to the H4MPT pathway that has primary importance. Studies on methylotrophy in Methylobacterium species have a long history, and this study provides further insights into genetic and physiological diversity and the differences in methylotrophy within the plant-colonizing methylotrophs.

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Section: The Mutation In Mxbd De-repress Mxafsupporting

confidence: 59%

Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A

et al. 2020

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“…Our work provides the first insights into the implications for cofactor electron transfer, necessary for enzyme activity in vivo, that are associated with substitution of lanthanides in XoxFs. Not only has nature developed sophisticated (and yet to be fully elucidated) mechanisms for selective uptake and regulation of light lanthanides—it has carefully tuned the redox properties of the MDH and its electron acceptor, XoxG, to prefer these metals over the later lanthanides. Furthermore, our characterization of the third and least understood member of the xox operon, XoxJ, provides a way forward in unraveling the mechanism of activation of MDHs with PQQ and metal ions.…”

Section: Resultsmentioning

confidence: 99%

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

et al. 2019

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Lanthanide (Ln)‐dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c‐type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with LaIII, CeIII, and NdIII using their physiological electron acceptor, XoxG, display Ln‐independent activities, but the Km for XoxG markedly increases from La to Nd. This result suggests that XoxG′s redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X‐ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG–XoxF interaction. Finally, the X‐ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.

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“…Further, the impact of iron is not identical for PedE and PedH-dependent growth (100 fold vs. 1000 fold). Since PedE regulation is solely dependent on PedS2 (Wehrmann et al, 2017; 2018), these data are thus supportive of such a mismetallation hypothesis, assuming that the sensor histidine kinase PedS2 and PedH have different binding affinities to La 3+ and/or Fe 2+/3+ .…”

Section: Discussionmentioning

confidence: 53%

“…Like many other organism, P. putida harbors an additional, Ln 3+ -independent functional homologue of PedH termed PedE that depends on a Ca 2+ ion as metal cofactor (Takeda et al, 2013; Wehrmann et al, 2017). Depending on the availability of REEs in the environment, P. putida tightly regulates PedE and PedH production (Wehrmann et al 2017, 2018). In the absence of Ln 3+ , growth is solely dependent on PedE whereas PedH transcription is repressed.…”

Section: Introductionmentioning

confidence: 99%

“…The situation immediately changes in the presence of small amounts of Ln 3+ (low nM range) leading to a strong induction of the Ln 3+ -dependent enzyme PedH and repression of its Ca 2+ -dependent counterpart PedE. For P. putida KT2440 the PedS2/PedR2 two component system (TCS) is a central component of this inverse regulation (Wehrmann et al, 2018). Notably, the REE-switch in P. putida was also found to be influenced by environmental conditions, as the critical La 3+ concentrations required to support PedH-dependent growth differs dramatically depending on the medium used, ranging from 5 nM up to 10 μM (Wehrmann et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Rare earth element (REE)-dependent growth of Pseudomonas putida KT2440 depends on the ABC-transporter PedA1A2BC and is influenced by iron availability

Wehrmann

Berthelot

Billard

et al. 2019

Preprint

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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. Expression 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 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 under environmental conditions with poor REE bioavailability. Our data further suggest that the La3+/Fe3+ 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 regards to REE-dependent phenomena.

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The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440

Cited by 33 publications

References 52 publications

Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A

Lanthanide-Dependent Methanol and Formaldehyde Oxidation in Methylobacterium aquaticum Strain 22A

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

Rare earth element (REE)-dependent growth of Pseudomonas putida KT2440 depends on the ABC-transporter PedA1A2BC and is influenced by iron availability

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