DadY (PA5303) is required for fitness of Pseudomonas aeruginosa when growth is dependent on alanine catabolism

Bulky substrates of isoleucine 2-epimerase: α-Neopentylglycine and NV-5138

Isoleucine 2-epimerase from Lactobacillus buchneri (LbIleE) catalyzes the pyridoxal 5'-phosphate-dependent, reversible, racemization or epimerization of nonpolar amino acids at the C-2 position. The integral role of the enzyme in the biosynthesis of branched-chain d-amino acids makes it a potential target for the development of antimicrobial agents. Probing the hydrophobic active-site pocket with a series of alkyl boronic acids, we show that the hydrophobic pocket accommodates the neopentyl group with enhanced binding affinity relative to the sec-butyl group. Subsequently, we show that LbIleE catalyzes the racemization of l- and d-α-neopentylglycine, exhibiting binding affinities for these substrates 6- and 24-fold greater than those for l-Ile and d-allo-Ile, but with catalytic efficiencies (kcat/Km) reduced 46- and 27-fold, respectively. NV-5138 is a ligand of the leucine-binding site of Sestrin2, which activates the mechanistic target of rapamycin complex1 (mTORC1) and is structurally similar to α-neopentylglycine. Our demonstration that LbIleE catalyzes the racemization of l-NV-5138 (kcat/Km = 2.2 ± 0.2 s-1 mM-1), along with the fact that L. buchneri can be present in the human gut microbiome, suggests that formation of d-NV-5138 could occur in humans when l-NV-5138 is used as a pharmacological intervention for depression.

Chemotaxis of rhizosphere Pseudomonas sp. induced by foliar spraying of lanthanum reduces cadmium uptake by pakchoi

Foliar application of rare earth micronutrient of lanthanum (La) exhibits great potential in reducing cadmium (Cd) uptake in crops, the underlying mechanisms controlling the interaction between Cd toxicity-relieved crops and soil microbiota are poorly understood. In this study, LaCl3 with the concentrations of 10 and 30 μM was sprayed on pakchoi (Brassica chinensis L.) planting on Cd contaminated solution and soil to determine the changes of root metabolites and rhizosphere bacterial communities. Compared to the control, Cd concentration in pakchoi leaves was significantly decreased by 30.9 % and 22.6 % with the high group under both hydroponic and pot culture by applying 30 μM LaCl3. Herein, the concrete evidence is provided that pakchoi plants in response to foliar-spraying La under soil or solution Cd toxicity can promote the root secretion of amino acids, resulting in a strong enrichment of nitrogen-related microorganisms. To probe this linkage, a Pseudomonas representative specie was isolated that had the ability of consuming alanine, the most oversecreted root exudate due to La application. Further results demonstrated that this strain had the capacities for alleviating Cd toxicity and enhancing crop growth by immobilizing Cd and secreting plant-beneficial metabolites. This study reveals a plant-extrudate-microbiome feedback loop for responding to La-relieved Cd toxicity in crops by the chemotaxis of rhizosphere Pseudomonas toward alanine secreted by pakchoi.

RidA proteins contribute to fitness of S. enterica and E. coli by reducing 2AA stress and moderating flux to isoleucine biosynthesis

Defining the physiological role of a gene product relies on interpreting phenotypes caused by the lack, or alteration, of the respective gene product. Mutations in critical genes often lead to easily recognized phenotypes that can include changes in cellular growth, metabolism, structure etc. However, mutations in many important genes may fail to generate an obvious defect unless additional perturbations are caused by medium or genetic background. The latter scenario is exemplified by RidA proteins. In vitro RidA proteins deaminate numerous imine/enamines, including those generated by serine/threonine dehydratase IlvA (EC:4.3.1.19) from serine or threonine - 2-aminoacrylate (2AA) and 2-aminocrotonate (2AC), respectively. Despite this demonstrable biochemical activity, a lack of RidA has little to no effect on growth of E. coli or S. enterica without the application of additional metabolic perturbation. A cellular role of RidA is to prevent accumulation of 2AA which, if allowed to persist, can irreversibly damage pyridoxal 5'-phosphate (PLP)-dependent enzymes, causing global metabolic stress. Because the phenotypes caused by a lack of RidA are dependent on the unique structure of each metabolic network, the link between RidA function and 2AA stress is difficult to demonstrate in some organisms. The current study used coculture experiments to exacerbate differences in growth caused by the lack of RidA in S. enterica and E. coli. Results described here solidify the established role of RidA in removing 2AA, while also presenting evidence for a role of RidA in enhancing flux towards isoleucine biosynthesis in E. coli. Overall, these data emphasize that metabolic networks can generate distinct responses to perturbation, even when the individual components are conserved.

Functional characterization of the dbu locus for D-branched-chain amino acid catabolism in Pseudomonas putida

Pseudomonas putida is a metabolically robust soil bacterium that employs a diverse set of pathways to utilize a wide range of nutrients. The versatility of this microorganism contributes to both its environmental ubiquity and its rising popularity as a bioengineering chassis. In P. putida, the newly named dbu locus encodes a transcriptional regulator (DbuR), D-amino acid oxidase (DbuA), Rid2 protein (DbuB), and a putative transporter (DbuC). Current annotation implicates this locus in the utilization of D-arginine. However, data obtained in this study showed that genes in the dbu locus are not required for D-arginine utilization, but, rather, this locus is involved in the catabolism of multiple D-branched-chain amino acids (D-BCAA). The oxidase DbuA was required for catabolism of each D-BCAA and D-phenylalanine, while the requirements for DbuC and DbuB were less stringent. The functional characterization of the dbu locus contributes to our understanding of the metabolic network of P. putida and proposes divergence in function between proteins annotated as D-arginine oxidases across the Pseudomonas genus.IMPORTANCEPseudomonas putida is a non-pathogenic bacterium that is broadly utilized as a host for bioengineering and bioremediation efforts. The popularity of P. putida as a chassis for such efforts is attributable to its physiological versatility and ability to metabolize a wide variety of compounds. Pathways for L-amino acid metabolism in this microbe have been rather well studied, primarily because of their relevance to efforts in foundational physiology research, as well as the commercial production of economically pertinent compounds. However, comparatively little is known about the metabolism of D-amino acids despite evidence showing the ability of P. putida to metabolize these enantiomers. In this work, we characterize the D-BCAA catabolic pathway of P. putida and its integration with the essential L-BCAA biosynthetic pathway. This work expands our understanding of the metabolic network of Pseudomonas putida, which has potential applications in efforts to model and engineer the metabolic network of this organism.

Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins

Metabolism is an integrated network of biochemical pathways that assemble to generate the robust, responsive physiologies of microorganisms. Despite decades of fundamental studies on metabolic processes and pathways, our understanding of the nuance and complexity of metabolism remains incomplete. The ability to predict and model metabolic network structure, and its influence on cellular fitness, is complicated by the persistence of genes of unknown function, even in the best-studied model organisms. This review describes the definition and continuing study of the Rid superfamily of proteins. These studies are presented with a perspective that illustrates how metabolic complexity can complicate the assignment of function to uncharacterized genes. The Rid superfamily of proteins has been divided into eight subfamilies, including the well-studied RidA subfamily. Aside from the RidA proteins, which are present in all domains of life and prevent metabolic stress, most members of the Rid superfamily have no demonstrated physiological role. Recent progress on functional assignment supports the hypothesis that, overall, proteins in the Rid superfamily modulate metabolic processes to ensure optimal organismal fitness.