A metabolic intermediate of the fructose-asparagine utilization pathway inhibits growth of a Salmonella fraB mutant

Identification of inhibitors of the Salmonella FraB deglycase, a drug target

Nontyphoidal Salmonella is one of the most prevalent causes of human foodborne illnesses worldwide, with no narrow-spectrum antibiotics or vaccines available. Here, we seek to address this gap. During the host inflammatory response, Salmonella metabolizes fructose-asparagine as a nutrient using proteins encoded in the fra operon. Deletion of fraB leads to a build-up of 6-phosphofructose-aspartate, the substrate of FraB, and intoxicates Salmonella. Because fra genes are absent in mammals and most members of the human gut microbiome, FraB inhibitors are expected to have limited off-target effects and offer prospects as potential therapeutics. To identify such inhibitors, we conducted a high-throughput screening of small-molecule libraries using a FraB activity-based biochemical assay. We screened 131,165 compounds and identified 126 hits that could be obtained commercially for further characterization. When tested at 25 μm inhibitor in the presence of 1 mm 6-phosphofructose-aspartate, FraB activity was reduced ~ 30-100% by 65 compounds. Guided by preliminary cell-based data, we further characterized six compounds (one triazolidine, two thiadiazolidines, and three triazolothiadiazoles) and found them to exhibit IC50 values from ~ 3 to 100 μm and KI (inhibitor constant) values from ~ 1 to 29 μm. Native mass spectrometry revealed that all three triazolothiadiazoles were capable of binding FraB; we also obtained evidence that one of the triazolothiadiazoles binds FraB even in the presence of substrate. The recurrence of multiple pharmacophores bolsters prospects for farming more hits from compound libraries and for designing therapeutics against nontyphoidal Salmonella.

Novel comprehensive perspective on Amadori compounds: preparation, multiple roles and interaction with other compounds

Amadori compounds are pivotal intermediates in the Maillard reaction. Amadori compounds serve as flavor enhancers, browning precursors and bioactive components, so they are promising versatile food additives. Comprehensive reviews on multiple roles of Amadori compounds are scarce. Furthermore, there is a lack of reviews on green, efficient and commercially prospective preparation techniques of Amadori compounds and their interactions with other components. This paper reviewed preparation, multiple roles and interactions with other components in foods. Spray drying, microwave heating, natural deep eutectic solvents and vacuum dewatering were deemed as green, efficient and commercially prospective preparation techniques for Amadori compounds. Amadori compounds broadened the application field of Maillard reaction-obtained additives compared to final-products, enabling their uses not only in dark-colored foodstuffs but also in light-colored. Peptide-derived Amadori compounds showed greater potency for flavor generation compared to amino acid-derived. Amadori compounds presented eleven physiological activities. Amadori compounds exerted synergistic effect with essential nutrients (lipids, exogenous amino acids and carbohydrates), functional ingredients (polyphenols, carotenoids, glycosides) as well as several drugs. More preparation approaches of Amadori compounds and their synergistic effects with other ingredients await investigation. This review provided comprehensive theoretical guidance for industrial preparation and application of Amadori compounds as versatile additives.

Novel insight into Amadori compounds: Fate of Amadori compounds in food supply chain

Amadori compounds, pivotal intermediates in the Maillard reaction, act as flavor enhancer, browning precursor, and functional component. Amadori compounds consisting of diverse amino and carbonyl groups might show distinct flavor attributes and functional activities. Food production involves many supply chain stages where thermal treatment might produce Amadori compounds, and processing techniques and circumstances might affect the generation and stability of Amadori compounds. Moreover, gastrointestinal digestion might also influence the stability of Amadori compounds. To date, there is a lack of comprehensive review on the impact of various supply chain stages and digestion on Amadori compounds. This paper reviewed all reported Amadori compounds derived from diverse reducing sugars (glucose, xylose, ribose, maltose) and amino-containing compounds (common and specific amino acids, peptides), and compared differences in synthetic efficiency, flavor property, and functional activity among them; aggregated qualitative techniques; encapsulated quantitative techniques including indirect quantification and direct quantification, and intuitively compared strengths and weaknesses of these techniques; and outlined influence of processing, cooking, storage, and digestion on formation and stability of Amadori compounds. Appropriate processing techniques and conditions favored the generation and stability of Amadori compounds. Baking, frying, and roasting greatly facilitated Amadori compounds accumulation compared to steaming and boiling. Prolonged cooking at relatively low temperature favored Amadori compounds accumulation, whereas high-temperature cooking for a short duration resulted in fewer accumulation. Amadori compounds showed greater digestion resistance and could be absorbed by the intestine. This review offers scientific instruction for producing high-quality products with abundant Amadori compounds, or extracting plentiful Amadori compounds from processed foods as versatile food additives.

MtlD as a therapeutic target for intestinal and systemic bacterial infections

The ability to treat infections is threatened by the rapid emergence of antibiotic resistance among pathogenic microbes. Therefore, new antimicrobials are needed. Here we evaluate mannitol-1-phosphate 5-dehydrogenase (MtlD) as a potential new drug target. In many bacteria, mannitol is transported into the cell and phosphorylated by MtlA, the EIICBA component of a phosphoenolpyruvate-dependent sugar phosphotransferase system. MtlD catalyzes the conversion of mannitol-1-phosphate (Mtl-1P) to fructose-6-phosphate, which enters the glycolytic pathway. Mutants lacking mtlD are sensitive to mannitol due to accumulation of Mtl-1P. Here, we constructed mtlD mutants in four different bacterial species (Cronobacter sakazakii, Pseudomonas aeruginosa, five serovars of Salmonella enterica, and three strains of Escherichia coli), confirming and quantifying their mannitol sensitivity. The quantification of mannitol sensitivity in vitro was complicated by an inoculum effect and a resumption of growth following mannitol intoxication. The rate of resumption at different mannitol concentrations and cell population densities is fairly constant and reveals what is likely an intoxication processing rate. Provision of mannitol in drinking water, or by intraperitoneal injection, dramatically attenuates infection of a Salmonella enterica serovar Typhimurium mtlD mutant in mouse models of both gastroenteritis and systemic infection. Using CC003/Unc mice, we find that a mtlD mutant of Salmonella enterica serovar Typhi is also attenuated by provision of mannitol in drinking water. Therefore, we postulate that MtlD could be a valuable new therapeutic target.

IMPORTANCE

The ability to treat infections is threatened by the rapid emergence of antibiotic resistance. Mannitol is a polyol used in human medicine and the food industry. During catabolism of mannitol, many bacteria transport mannitol across the inner membrane forming the toxic intermediate mannitol-1-phosphate (Mtl-1P). Mtl-1P must be processed by mannitol dehydrogenase (MtlD) or it accumulates intracellularly, causing growth attenuation. We test and confirm here that mtlD mutants of Escherichia coli (including UPEC, and EHEC), Salmonella (including serovars Typhi, and Paratyphi A, B, and C), Cronobacter, and Pseudomonas experience mannitol sensitivity in vitro. Furthermore, providing mannitol in drinking water can alleviate both gastrointestinal and systemic Salmonella infections in mice. This suggests that inhibition of MtlD could be a viable antimicrobial strategy.

Lethal metabolism of Candida albicans respiratory mutants

The destructive impact of fungi in agriculture and animal and human health, coincident with increases in antifungal resistance, underscores the need for new and alternative drug targets to counteract these trends. Cellular metabolism relies on many intermediates with intrinsic toxicity and promiscuous enzymatic activity generates others. Fuller knowledge of these toxic entities and their generation may offer opportunities of antifungal development. From this perspective our observation of media-conditional lethal metabolism in respiratory mutants of the opportunistic fungal pathogen Candida albicans was of interest. C. albicans mutants defective in NADH:ubiquinone oxidoreductase (Complex I of the electron transport chain) exhibit normal growth in synthetic complete medium. In YPD medium, however, the mutants grow normally until early stationary phase whereupon a dramatic loss of viability occurs. Upwards of 90% of cells die over the subsequent four to six hours with a loss of membrane integrity. The extent of cell death was proportional to the amount of BactoPeptone, and to a lesser extent, the amount of yeast extract. YPD medium conditioned by growth of the mutant was toxic to wild-type cells indicating mutant metabolism established a toxic milieu in the media. Conditioned media contained a volatile component that contributed to toxicity, but only in the presence of a component of BactoPeptone. Fractionation experiments revealed purine nucleosides or bases as the synergistic component. GC-mass spectrometry analysis revealed acetal (1,1-diethoxyethane) as the active volatile. This previously unreported and lethal synergistic interaction of acetal and purines suggests a hitherto unrecognized toxic metabolism potentially exploitable in the search for antifungal targets.

1-Amino-1-deoxy-d-fructose ("fructosamine") and its derivatives: An update

1-Amino-1-deoxy-d-fructose (fructosamine, FN) derivatives are omnipresent in all living organisms, as a result of non-enzymatic condensation and Amadori rearrangement reactions between free glucose and biogenic amines such as amino acids, polypeptides, or aminophospholipids. Over decades, steady interest in fructosamine was largely sustained by its role as a key intermediate structure in the Maillard reaction that is responsible for the organoleptic and nutritional value of thermally processed foods, and for pathophysiological effects of hyperglycemia in diabetes. New trends in fructosamine research include the discovery and engineering of FN-processing enzymes, development of advanced tools for hyperglycemia monitoring, and evaluation of the therapeutic potential of both fructosamines and FN-recognizing proteins. This article covers developments in the field of fructosamine and its derivatives since 2010 and attempts to ascertain challenges in future research.

Amadori compounds: analysis, composition in food and potential health beneficial functions

Amadori compounds (ACs) are key intermediates of the Maillard reaction, and found in various thermally processed foods. Simultaneous analysis of multiple ACs is challenging due to the complex amino acid and carbohydrate compositions, and the different food matrices. Most studies focus on the effects of ACs on food flavor and related sensory properties, but not their biological functions. However, increasing evidence shows that ACs possess various beneficial effects on human health, thus a comprehensive review on the various biological activities is warranted. In this review, we summarized the composition and content of ACs in different foods, their formation and degradation reactions, and discussed the latest advances in analytical methods of ACs and their biological functions related to human health. Limitations and research gaps were identified and future perspectives on ACs research were proposed. This review points to the needs of systematic and comprehensive in vitro and in vivo studies on human health related biological functions of ACs and their mechanisms of action, particularly the synergistic effects with other food components and drugs, and roles in intestinal health and metabolic syndrome.

Demonstrating the utility of sugar-phosphate phosphatases in coupled enzyme assays: galactose-1-phosphate uridylyltransferase as proof-of-concept

During our biochemical characterization of select bacterial phosphatases belonging to the haloacid dehalogenase superfamily of hydrolases, we discovered a strong bias of Salmonella YidA for glucose-1-phosphate (Glc-1-P) over galactose-1-phosphate (Gal-1-P). We sought to exploit this ability of YidA to discriminate these two sugar-phosphate epimers in a simple coupled assay that could be a substitute for current cumbersome alternatives. To this end, we focused on Gal-1-P uridylyltransferase (GalT) that is defective in individuals with classical galactosemia, an inborn disorder. GalT catalyzes the conversion of Gal-1-P and UDP-glucose to Glc-1-P and UDP-galactose. When recombinant YidA was coupled to GalT, the final orthophosphate product (generated from selective hydrolysis of Glc-1-P by YidA) could be easily measured using the inexpensive malachite green reagent. When this new YidA-based colorimetric assay was benchmarked using a recombinant Duarte GalT variant, it yielded kcat/Km values that are ~2.5-fold higher than the standard coupled assay that employs phosphoglucomutase and glucose-6-phosphate dehydrogenase. Although the simpler design of our new GalT coupled assay might find appeal in diagnostics, a testable expectation, we spotlight the GalT example to showcase the untapped potential of sugar-phosphate phosphatases with distinctive substrate-recognition properties for measuring the activity of various metabolic enzymes (e.g. trehalose-6-phosphate synthase, N-acetyl-glucosamine-6-phosphate deacetylase, phosphofructokinase).

Identification of Small-Molecule Inhibitors of the Salmonella FraB Deglycase Using a Live-Cell Assay

Nontyphoidal salmonellosis is one of the most significant foodborne diseases in the United States and globally. There are no vaccines available for human use to prevent this disease, and only broad-spectrum antibiotics are available to treat complicated cases of the disease. However, antibiotic resistance is on the rise and new therapeutics are needed. We previously identified the Salmonella fraB gene, that mutation of causes attenuation of fitness in the murine gastrointestinal tract. The FraB gene product is encoded in an operon responsible for the uptake and utilization of fructose-asparagine (F-Asn), an Amadori product found in several human foods. Mutations in fraB cause an accumulation of the FraB substrate, 6-phosphofructose-aspartate (6-P-F-Asp), which is toxic to Salmonella. The F-Asn catabolic pathway is found only in the nontyphoidal Salmonella serovars, a few Citrobacter and Klebsiella isolates, and a few species of Clostridium; it is not found in humans. Thus, targeting FraB with novel antimicrobials is expected to be Salmonella specific, leaving the normal microbiota largely intact and having no effect on the host. We performed high-throughput screening (HTS) to identify small-molecule inhibitors of FraB using growth-based assays comparing a wild-type Salmonella and a Δfra island mutant control. We screened 224,009 compounds in duplicate. After hit triage and validation, we found three compounds that inhibit Salmonella in an fra-dependent manner, with 50% inhibitory concentration (IC50) values ranging from 89 to 150 μM. Testing these compounds with recombinant FraB and synthetic 6-P-F-Asp confirmed that they are uncompetitive inhibitors of FraB with Ki' (inhibitor constant) values ranging from 26 to 116 μM. IMPORTANCE Nontyphoidal salmonellosis is a serious threat in the United States and globally. We have recently identified an enzyme, FraB, that when mutated renders Salmonella growth defective in vitro and unfit in mouse models of gastroenteritis. FraB is quite rare in bacteria and is not found in humans or other animals. Here, we have identified small-molecule inhibitors of FraB that inhibit the growth of Salmonella. These could provide the foundation for a therapeutic to reduce the duration and severity of Salmonella infections.

Inducing Self-Poisoning: a Feasible Antibacterial Strategy?

Development of novel antibacterial strategies is required to tackle the alarming threat for global health due to antimicrobial resistance. In this issue of the Journal of Bacteriology, Boulanger et al. provide evidence supporting that the blocking of metabolic pathways to induce accumulation of toxic intermediates can be a possible approach to combat bacterial infections (E. F. Boulanger, A. Sabag-Daigle, M. Baniasad, K. Kokkinias, et al., J Bacteriol 204:e00344-22, 2022, https://doi.org/10.1128/jb.00344-22).

Sugar-Phosphate Toxicities Attenuate Salmonella Fitness in the Gut

Pathogens are becoming resistant to antimicrobials at an increasing rate, and novel therapeutic strategies are needed. Using Salmonella as a model, we have investigated the induction of sugar-phosphate toxicity as a potential therapeutic modality. The approach entails providing a nutrient while blocking the catabolism of that nutrient, resulting in the accumulation of a toxic intermediate. We hypothesize that this build-up will decrease the fitness of the organism during infection given nutrient availability. We tested this hypothesis using mutants lacking one of seven genes whose mutation is expected to cause the accumulation of a toxic metabolic intermediate. The araD, galE, rhaD, glpD, mtlD, manA, and galT mutants were then provided the appropriate sugars, either in vitro or during gastrointestinal infection of mice. All but the glpD mutant had nutrient-dependent growth defects in vitro, suggestive of sugar-phosphate toxicity. During gastrointestinal infection of mice, five mutants had decreased fitness. Providing the appropriate nutrient in the animal's drinking water was required to cause fitness defects with the rhaD and manA mutants and to enhance the fitness defect of the araD mutant. The galE and mtlD mutants were severely attenuated regardless of the nutrient being provided in the drinking water. Homologs of galE are widespread among bacteria and in humans, rendering the specific targeting of bacterial pathogens difficult. However, the araD, mtlD, and rhaD genes are not present in humans, appear to be rare in most phyla of bacteria, and are common in several genera of Enterobacteriaceae, making the encoded enzymes potential narrow-spectrum therapeutic targets. IMPORTANCE Bacterial pathogens are becoming increasingly resistant to antibiotics. There is an urgent need to identify novel drug targets and therapeutic strategies. In this work we have assembled and characterized a collection of mutations in our model pathogen, Salmonella enterica, that block a variety of sugar utilization pathways in such a way as to cause the accumulation of a toxic sugar-phosphate. Mutations in three genes, rhaD, araD, and mtlD, dramatically decrease the fitness of Salmonella in a mouse model of gastroenteritis, suggesting that RhaD, AraD, and MtlD may be good narrow-spectrum drug targets. The induction of sugar-phosphate toxicities may be a therapeutic strategy that is broadly relevant to other bacterial and fungal pathogens.

Formation of Amadori compounds in LIGAO (concentrated pear juice) processing and the effects of Fru-Asp on cough relief and lung moisturization in mice

LIGAO (concentrated pear juice) has been used for more than 1000 years to treat respiratory complaints such as cough and expectoration in China, but the study of the mechanism of its antitussive effects and ability to moisten the lungs is limited. This study found that the content of Amadori compounds (ACs) and other nutrients changed during LIGAO processing. Furthermore, N-(1-deoxy-D-fructos-1-yl)-aspartic acid (Fru-Asp), the most abundant and characteristic AC in LIGAO, was prepared and studied. The antitussive test revealed that Fru-Asp could significantly reduce the frequency of cough and prolong the cough latent period in mice. A high dose of Fru-Asp (250 mg kg^-1) in mice provided better therapeutic activities than that of dextromethorphan hydrobromide tablets (30 mg kg^-1). In the Fru-Asp pretreated group, Fru-Asp significantly alleviated inflammation in LPS-induced acute lung injury mice. Fru-Asp can significantly decrease the levels of TNF-α and IL-β in mice by 11%. Additionally, Fru-Asp exhibited angiotensin-converting enzyme (ACE) inhibitor activity (IC₅₀ = 0.242 mM). The contribution and health benefits of Fru-Asp on cough relief were first reported in this study, which also substantiated it as a functional component of LIGAO. The results provided the basis for future research on the health effects of ACs and a method to improve the added value of LIGAO and other pear products.

Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target

Although salmonellosis, an infectious disease, is a significant global healthcare burden, there are no Salmonella-specific vaccines or therapeutics for humans. Motivated by our finding that FraB, a Salmonella deglycase responsible for fructose-asparagine catabolism, is a viable drug target, we initiated experimental and computational efforts to identify inhibitors of FraB. To this end, our recent high-throughput screening initiative yielded almost exclusively uncompetitive inhibitors of FraB. In parallel with this advance, we report here how a separate structural and computational biology investigation of FrlB, a FraB paralog, led to the serendipitous discovery that 2-deoxy-6-phosphogluconate is a competitive inhibitor of FraB (KI ~ 3 μM). However, this compound was ineffective in inhibiting the growth of Salmonella in a liquid culture. In addition to poor uptake, cellular metabolic transformations by a Salmonella dehydrogenase and different phosphatases likely undermined the efficacy of 2-deoxy-6-phosphogluconate in live-cell assays. These insights inform our ongoing efforts to synthesize non-hydrolyzable/-metabolizable analogs of 2-deoxy-6-phosphogluconate. We showcase our findings largely to (re)emphasize the role of serendipity and the importance of multi-pronged approaches in drug discovery.

Effect of diet on pathogen performance in the microbiome

Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.

Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry

FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.

Sugar-Phosphate Toxicities

Accumulation of phosphorylated intermediates during cellular metabolism can have wide-ranging toxic effects on many organisms, including humans and the pathogens that infect them. These toxicities can be induced by feeding an upstream metabolite (a sugar, for instance) while simultaneously blocking the appropriate metabolic pathway with either a mutation or an enzyme inhibitor. Here, we survey the toxicities that can arise in the metabolism of glucose, galactose, fructose, fructose-asparagine, glycerol, trehalose, maltose, mannose, mannitol, arabinose, and rhamnose. Select enzymes in these metabolic pathways may serve as novel therapeutic targets. Some are conserved broadly among prokaryotes and eukaryotes (e.g., glucose and galactose) and are therefore unlikely to be viable drug targets. However, others are found only in bacteria (e.g., fructose-asparagine, rhamnose, and arabinose), and one is found in fungi but not in humans (trehalose). We discuss what is known about the mechanisms of toxicity and how resistance is achieved in order to identify the prospects and challenges associated with targeted exploitation of these pervasive metabolic vulnerabilities.

Vacuum Dehydration: An Excellent Method to Promote the Formation of Amadori Compounds (ACs, N-(1-Deoxy-d-fructos-1-yl)-amino Acid) in Aqueous Models and Tomato Sauce

Amadori compounds (ACs; N-(1-deoxy-d-fructos-1-yl)-amino acid) are superior flavor precursors and potential functional ingredients in food processing. In this study, vacuum dehydration as an excellent and universal method for the formation of ACs in both simulation systems and food processing was revealed. In total, 12 amino acids referring to all six categories were selected to conduct simulated reactions with glucose in aqueous models. At 90 °C, yields of 11 ACs were significantly increased by vacuum dehydration, reaching 4-198 times compared to a heat sealing reaction in aqueous systems, and formation of 5-hydroxymethyl-2-furaldehyde (5-HMF) and browning were slower than that by a dry powder reaction. In particular, the yields of Fru-Arg, Fru-His, and Fru-Glu reached 87.03, 90.73, and 89.88 mol %, respectively. The order of promotion effect was acid ACs > basic ACs > unique ACs > polar neutral ACs > aliphatic ACs > aromatic ACs. The excellent effect was mainly attributed to the control of water activity (Aw) and pH, which enabled the models to reach the optimal reaction state quickly by adjusting the vacuum degree at mild temperatures. The method was also applied to AC enrichment in tomato sauce processing; the AC content could rise to 30.72 mg/g, which was more than 17 times than those in samples without vacuum dehydration and two commercial tomato sauces.

Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase

Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including the terminal FraB deglycase. Salmonella mutants lacking FraB are highly attenuated in mouse models of inflammation due to the toxic build-up of the substrate 6-phosphofructose-aspartate (6-P-F-Asp). This toxicity makes Salmonella FraB an appealing drug target, but there is currently little experimental information about its catalytic mechanism. Therefore, we sought to test our postulated mechanism for the FraB-catalyzed deglycation of 6-P-F-Asp (via an enaminol intermediate) to glucose-6-phosphate and aspartate. A FraB homodimer model generated by RosettaCM was used to build substrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putative active site. Five candidate active-site residues-including three expected to participate in substrate binding-were mutated individually and characterized. Native mass spectrometry and ion mobility were used to assess collision cross sections and confirm that the quaternary structure of the mutants mirrored the wild type, and that there are two active sites/homodimer. Our biochemical studies revealed that FraB Glu214Ala, Glu214Asp, and His230Ala were inactive in vitro, consistent with deprotonated-Glu214 and protonated-His230 serving as a general base and a general acid, respectively. Glu214Ala or His230Ala introduced into the Salmonella chromosome by CRISPR/Cas9-mediated genome editing abolished growth on F-Asn. Results from our computational and experimental approaches shed light on the catalytic mechanism of Salmonella FraB and of phosphosugar deglycases in general.

Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut

Salmonella enterica elicits intestinal inflammation to gain access to nutrients. One of these nutrients is fructose-asparagine (F-Asn). The availability of F-Asn to Salmonella during infection is dependent upon Salmonella pathogenicity islands 1 and 2, which in turn are required to provoke inflammation. Here, we determined that F-Asn is present in mouse chow at approximately 400 pmol/mg (dry weight). F-Asn is also present in the intestinal tract of germfree mice at 2,700 pmol/mg (dry weight) and in the intestinal tract of conventional mice at 9 to 28 pmol/mg. These findings suggest that the mouse intestinal microbiota consumes F-Asn. We utilized heavy-labeled precursors of F-Asn to monitor its formation in the intestine, in the presence or absence of inflammation, and none was observed. Finally, we determined that some members of the class Clostridia encode F-Asn utilization pathways and that they are eliminated from highly inflamed Salmonella-infected mice. Collectively, our studies identify the source of F-Asn as the diet and that Salmonella-mediated inflammation is required to eliminate competitors and allow the pathogen nearly exclusive access to this nutrient.

Identification of Bacterial Species That Can Utilize Fructose-Asparagine

Salmonella enterica serovar Typhimurium is the only organism demonstrated to utilize fructose-asparagine (F-Asn) as a source of carbon and nitrogen. In this report, we first used a bioinformatics approach to identify other microorganisms that encode homologs of the Salmonella F-Asn utilization enzymes FraB (deglycase), FraD (kinase), and FraE (asparaginase). These candidate organisms were then tested with up to four different methods to confirm their ability to utilize F-Asn. The easiest and most broadly applicable method utilized a biological toxicity assay, which is based on the observation that F-Asn is toxic to a Salmonella fraB mutant. Candidate organisms were grown in a rich medium containing F-Asn, and depletion of F-Asn from the medium was inferred by the growth of a Salmonella fraB mutant in that same medium. For select organisms, the toxicity assay was cross-validated by direct mass spectrometry-aided measurement of F-Asn in the spent-culture media and through demonstration of FraB and FraD enzyme activity in cellular extracts. For prototrophs, F-Asn utilization was additionally confirmed by growth in a minimal medium containing F-Asn as the sole carbon source. Collectively, these studies established that Clostridiumbolteae, Clostridium acetobutylicum, and Clostridium clostridioforme can utilize F-Asn, but Clostridium difficile cannot; Klebsiella oxytoca and some Klebsiella pneumoniae subspecies can utilize F-Asn; and some Citrobacter rodentium and Citrobacter freundii strains can also utilize F-Asn. Within Salmonella enterica, the host-adapted serovars Typhi and Paratyphi A have lost the ability to utilize F-Asn.IMPORTANCE Fructose-asparagine (F-Asn) is a precursor to acrylamide that is found in human foods, and it is also a nutrient source for Salmonella enterica, a foodborne pathogen. Here, we determined that among the normal intestinal microbiota, there are species of Clostridium that encode the enzymes required for F-Asn utilization. Using complementary experimental approaches, we have confirmed that three members of Clostridium, two members of Klebsiella, and two members of Citrobacter can indeed utilize F-Asn. The Clostridium spp. likely compete with Salmonella for F-Asn in the gut and contribute to competitive exclusion. FraB, one of the enzymes in the F-Asn utilization pathway, is a potential drug target because inhibition of this enzyme leads to the accumulation of a toxic metabolite that inhibits the growth of Salmonella species. This study identifies the potential off-target organisms that need to be considered when developing therapeutics directed at FraB.

Measurement of Fructose-Asparagine Concentrations in Human and Animal Foods

The food-borne bacterial pathogen, Salmonella enterica, can utilize fructose-asparagine (F-Asn) as its sole carbon and nitrogen source. F-Asn is the product of an Amadori rearrangement following the nonenzymatic condensation of glucose and asparagine. Heating converts F-Asn via complex Maillard reactions to a variety of molecules that contribute to the color, taste, and aroma of heated foods. Among these end derivatives is acrylamide, which is present in some foods, especially in fried potatoes. The F-Asn utilization pathway in Salmonella, specifically FraB, is a potential drug target because inhibition of this enzyme would lead to intoxication of Salmonella in the presence of F-Asn. However, F-Asn would need to be packaged with the FraB inhibitor or available in human foods. To determine if there are foods that have sufficient F-Asn, we measured F-Asn concentrations in a variety of human and animal foods. The 400 pmol/mg F-Asn found in mouse chow is sufficient to intoxicate a Salmonella fraB mutant in mouse models of salmonellosis, and several human foods were found to have F-Asn at this level or higher (fresh apricots, lettuce, asparagus, and canned peaches). Much higher concentrations (11 000-35 000 pmol/mg dry weight) were found in heat-dried apricots, apples, and asparagus. This report reveals possible origins of F-Asn as a nutrient source for Salmonella and identifies foods that could be used together with a FraB inhibitor as a therapeutic agent for Salmonella.

Salmonella FraE, an Asparaginase Homolog, Contributes to Fructose-Asparagine but Not Asparagine Utilization

Salmonella enterica can utilize fructose-asparagine (F-Asn) as a source of carbon and nitrogen. This capability has been attributed to five genes in the fra locus. Previously, we determined that mutations in fraB (deglycase), fraD (kinase), or fraA (transporter) eliminated the ability of Salmonella to grow on F-Asn, while a mutation in fraE allowed partial growth. We hypothesized that FraE, a putative periplasmic fructose-asparaginase, converts F-Asn to NH₄ ⁺ and fructose-aspartate (F-Asp). FraA could then transport F-Asp into the cytoplasm for subsequent catabolism. Here, we report that growth of the fraE mutant on F-Asn is caused by a partially redundant activity provided by AnsB, a periplasmic asparaginase. Indeed, a fraE ansB double mutant is unable to grow on F-Asn. Moreover, biochemical assays using periplasmic extracts of mutants that express only FraE or AnsB confirmed that each of these enzymes converts F-Asn to F-Asp and NH₄ ⁺ However, FraE does not contribute to growth on asparagine. We tested and confirmed the hypothesis that a fraE ansB mutant can grow on F-Asp, while mutants lacking fraA, fraD, or fraB cannot. This finding provides strong evidence that FraA transports F-Asp but not F-Asn from the periplasm to the cytoplasm. Previously, we determined that F-Asn is toxic to a fraB mutant due to the accumulation of the FraB substrate, 6-phosphofructose-aspartate (6-P-F-Asp). Here, we found that, as expected, a fraB mutant is also inhibited by F-Asp. Collectively, these findings contribute to a better understanding of F-Asn utilization by Salmonella IMPORTANCE Salmonella is able to utilize fructose-asparagine (F-Asn) as a nutrient. We recently reported that the disruption of a deglycase enzyme in the F-Asn utilization pathway inhibits the growth of Salmonella in mice and recognized this pathway as a novel and specific drug target. Here, we characterize the first step in the pathway wherein FraE hydrolyzes F-Asn to release NH₄ ⁺ and F-Asp in the periplasm of the cell. A fraE mutant continues to grow slowly on F-Asn due to asparaginase activity encoded by ansB.

Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation

Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.

A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid

Many microorganisms produce phosphonates, molecules characterized by stable carbon-phosphorus bonds that store phosphorus or act as antimicrobials. The role of phosphonates in the marine biosphere is well characterized but the role of these molecules in the intestine is poorly understood. Salmonella enterica uses its virulence factors to influence the host immune response to compete with the host and normal microflora for nutrients. Salmonella cannot produce phosphonates but encodes the enzymes to use them suggesting that it is exposed to phosphonates during its life cycle. The role of phosphonates during enteric salmonellosis is unexplored. We have previously shown that STM3602, encoding a putative regulator of phosphonate metabolism, is needed for colonization in calves. Here, we report that the necessity of STM3602 in colonization of the murine intestine results from multiple factors. STM3602 is needed for full activation of the type-3 secretion system-1 and for optimal invasion of epithelial cells. The ΔSTM3602 mutant grows poorly in phosphonoacetic acid (PA) as the sole phosphorus source, but can use 2-aminoethylphosphonate. PhnA, an enzyme required for PA breakdown, is not controlled by STM3602 suggesting an additional mechanism for utilization of PA in S. Typhimurium. Finally, the requirement of STM3602 for intestinal colonization differs depending on the composition of the microflora. Our data suggest that STM3602 has multiple regulatory targets that are necessary for survival within the microbial community in the intestine. Determination of the members of the STM3602 regulon may illuminate new pathways needed for colonization of the host.

Characterization of a Salmonella sugar kinase essential for the utilization of fructose-asparagine

Salmonella can utilize fructose-asparagine (F-Asn), a naturally occurring Amadori product, as its sole carbon and nitrogen source. Conversion of F-Asn to the common intermediates glucose-6-phosphate, aspartate, and ammonia was predicted to involve the sequential action of an asparaginase, a kinase, and a deglycase. Mutants lacking the deglycase are highly attenuated in mouse models of intestinal inflammation owing to the toxic build-up of the deglycase substrate. The limited distribution of this metabolic pathway in the animal gut microbiome raises the prospects for antibacterial discovery. We report the biochemical characterization of the kinase that was expected to transform fructose-aspartate to 6-phosphofructose-aspartate during F-Asn utilization. In addition to confirming its anticipated function, we determined through studies of fructose-aspartate analogues that this kinase exhibits a substrate-specificity with greater tolerance to changes to the amino acid (including the d-isomer of aspartate) than to the sugar.