Solute carrier (SLC) transport proteins are fundamental for the translocation of endogenous compounds and drugs across membranes, thus playing a critical role in disease susceptibility and drug response. Because only a limited number of transporter substrates are currently known, the function of a large number of SLC transporters is elusive. Here, we describe the proof-of-concept of a novel strategy to identify SLC transporter substrates exemplarily for the proton-coupled peptide transporter (PEPT) 2 (SLC15A2) and multidrug and toxin extrusion (MATE) 1 transporter (SLC47A1), which are important renal transporters of drug reabsorption and excretion, respectively. By combining metabolomic profiling of mice with genetically-disrupted transporters, in silico ligand screening and in vitro transport studies for experimental validation, we identified nucleobases and nucleosidederived anticancer and antiviral agents (flucytosine, cytarabine, gemcitabine, capecitabine) as novel drug substrates of the MATE1 transporter. Our data confirms the successful applicability of this new approach for the identification of transporter substrates in general, which may prove particularly relevant in drug research.

A correction to this paper has been published: https://doi.org/10.1007/s11306-021-01784-5

We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30–90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org .

Targeted analysis of Coffea arabica and Coffea canephora green coffees (total sample size n = 57) confirmed 2- O-β-d-glucopyranosyl-carboxyatractyligenin (6) as the quantitatively dominating carboxyatractyligenin derivative. Its abundance in Arabicas (2425 ± 549 nmol/g, n = 48) exceeded that in Robustas (34 ± 12 nmol/g, n = 9) roughly by a factor of 70. Coffee processing involving heat (e.g., steam treatment and decaffeination) reduced concentrations of 6 and increased those of the decarboxylated derivative. The bioavailability of compound 6 in Caenorhabditis elegans was demonstrated by ultraperformance liquid chromatography-tandem mass spectrometry analysis of extracts prepared from nematode cultures incubated in a liquid medium containing 6. A toxicity assay performed to assess the impact of 6 in vivo showed a 20-fold higher median lethal dose (LD50 = 11.7 ± 1.2 mM) concentration compared to that of the known phytotoxic adenine-nucleotide transporters inhibitor carboxyatractyloside (2, LD50 = 0.61 ± 0.05 mM), whereas 1 mM 6 and 0.1 mM 2 were sufficient to decrease the survival of wild type C. elegans, already 10-20-fold lower doses reduced reproduction. Because the insulin/insulin-like growth factors signaling cascade (IIS) is a key regulator of life span and stress resistance, the impact of compound 6 on the survival of long-living daf-2 C. elegans was tested. As the susceptibility of these nematodes to 6 was as high as that in wild type, an impact on central metabolic processes independent of IIS was suggested. Analysis of the in vivo adenosine triphosphate (ATP) content of adult C. elegans revealed no changes after 1 and 24 h, but a 50% reduction after treatment with 1 mM 6 during the entire postembryonic development. These data speak for a developmental-stage-dependent modulation of the ATP pool by 6.

Scope The role of PEPT1 in the uptake of intact peptides as compared to hydrolysis prior to uptake of their constituents is unknown. Here, dipeptides, tripeptides, and amino acids are quantified to study the fate of selected peptides in different intestinal models. Methods and results An LC-MS/MS-based method is applied for the simultaneous assessment of rates of hydrolysis and transport of a peptide panel in Caco-2 transwell cell culture, in vitro and in vivo in mice expressing or lacking PEPT1, and in hydrolysis studies in vitro using human intestinal samples. It is shown that susceptibility to hydrolysis of peptides at the brush border membrane or within epithelial cells is practically identical in all tested models and strictly structure-dependent. Peptides with high luminal disappearance show substantial hydrolysis and low basolateral appearance, while peptides with low disappearance show strong PEPT1 dependency and high basolateral appearance in intact form in Caco-2 transwell culture. Conclusion Hydrolysis and transport of intact peptides are highly variable and structure-dependent. For peptides possessing less polar N-terminal residues, hydrolysis usually dominates over transport via PEPT1. For other peptides with high intrinsic hydrolysis resistance, including anserine, carnosine, gamma-glutamyl-dipeptides, and aminocephalosporins, PEPT1 is the main determinant for appearance in peripheral blood.

As the organ with one of the largest surface areas facing the environment and responsible for nutrient uptake, the small intestine expresses numerous transport proteins in its brush-border membrane for efficient absorption and supply of dietary macro- and micronutrients. The understanding of regulation and functional interplay of these nutrient transporters is of emerging interest in nutrition and medical physiology research in respect to development of diabetes, obesity, and inflammatory bowel disease worldwide. The peptide transporter 1 (PepT1, SLC15A1) is abundantly expressed particularly in the intestinal tract and provides highly effective transport of amino acids in the form of di- and tripeptides and features a substantial acceptance for structurally related compounds and drugs. These characteristics bring PepT1 into focus for nutritional and medical/pharmaceutical approaches, as it is the essential hub responsible for oral bioavailability of dietary protein/peptide supplements and peptide-like drugs in eukaryotic organisms. Detailed analysis of molecular processes regulating PepT1 expression and function achieved in the last two decades has helped to define and use adjusting tools and to better integrate the transporter's role in cell and organ physiology. In this article, we provide an overview of the current knowledge on PepT1 function in health and disease, and on regulatory factors modulating its gene and protein expression as well as transport activity. © 2018 American Physiological Society. Compr Physiol 8:843-869, 2018.

Abstract The pre-implantation period is prone to embryonic losses in bovine. Embryo–maternal communication is crucial to support embryo development. Thereby, factors of the uterine fluid (UF) are of specific importance. The maternal diet can affect the UF composition. Since omega 3 fatty acids (omega 3 FA) are considered to be beneficial for reproduction, we investigated if dietary omega 3 FA affected factors in the UF related to embryo elongation. Angus heifers (n = 37) were supplemented with either 450 g of rumen-protected fish oil (omega 3 FA) or sunflower oil (omega 6 FA) for a period of 8 weeks. Following cycle synchronization and artificial insemination, the uteri were flushed post mortem to recover the embryos on day 15 of pregnancy. The UF and tissue samples of endometrium and corpus luteum (CL) were collected. Strikingly, the embryo elongation in the omega 3 group was enhanced compared to the omega 6 group. No differences were observed in uterine prostaglandins, even though the endometrial concentration of their precursor arachidonic acidwas reduced in omega 3 compared to omega 6 heifers. The dietary FA neither led to differential expression of target genes in endometrium nor CL nor to a differential abundance of low-density lipoprotein cholesterol, cortisol or amino acids in the UF. Interestingly, the omega 3 group displayed a higher plasma progesterone concentration during luteal growth than the omega 6 group, possibly promoting embryo elongation. Further research should include an ovarian perspective to understand the functional link between dietary omega 3 FA and reproductive outcome. Summary Sentence The pre-implantation embryo elongation in bovine is affected by dietary omega 3/6 fatty acids likely due to an effect on the ovary rather than a change of the uterine secretome.

The New Zealand obese (NZO) mouse is a polygenic model for obesity and diabetes with obese females and obese, diabetes-prone males, used to study traits of the metabolic syndrome like type 2 diabetes mellitus (T2DM), obesity, and dyslipidaemia. By using LC-MS/MS, we here examine the suitability of this model to mirror tissue-specific changes in acylcarnitine (AC) and amino acid (AA) species preceding T2DM which may reflect patterns investigated in human metabolism. We observed high concentrations of fatty acid-derived ACs in 11 female mice, high abundance of branched-chain amino acid- (BCAA-) derived ACs in 6 male mice, and slight increases in BCAA-derived ACs in the remaining 6 males. Principal component analysis (PCA) including all ACs and AAs confirmed our hypothesis especially in plasma samples by clustering females, males with high BCAA-derived ACs, and males with slight increases in BCAA-derived ACs. Concentrations of insulin, blood glucose, NEFAs, and triacylglycerols (TAGs) further supported the hypothesis of high BCAA-derived ACs being able to mirror the onset of diabetic traits in male individuals. In conclusion, alterations in AC and AA profiles overlap with observations from human studies indicating the suitability of NZO mice to study metabolic changes preceding human T2DM.

SCOPEPeptide transporter 1 (PEPT1) function is well understood, yet little is known about its contribution toward the absorption of dietary amino acids in the form of di- and tripeptides. In the present human study, changes in plasma concentrations of a representative oligopeptide panel are investigated after meat intake.METHODS AND RESULTSBased on a method for quantitative analysis of a panel of selected di- and tripeptides in biological samples, the kinetics of plasma changes of peptides derived from a widely accessible dietary protein source are described. The findings demonstrate postprandial changes of a whole spectrum of dipeptides of different size, charge, and polarity in peripheral blood in a dose-dependent manner after consumption of chicken breast in healthy human volunteers. Although the substrate specificity of PEPT1 is well known, the spectrum of peptides appearing in blood cannot be matched to the affinity to PEPT1. Stability against hydrolysis by exo- and endopeptidases appears to be another factor influencing their presence in blood. In addition, the study shows that dipeptides, including gamma-glutamyl-peptides, as well as tripeptides are common components present in human plasma.CONCLUSIONBesides amino acids, human peripheral blood contains numerous di- and tripeptides. The dietary source determines their abundance and composition.

Intestinal absorption of dietary amino acids is mediated via two routes. Free amino acids released by hydrolysis of dietary proteins are taken up by a multitude of amino acid transporters while di- and tripeptides released are taken up by the peptide transporter PEPT-1. Loss of PEPT-1 impairs growth, post-embryonic development and reproduction in Caenorhabditis elegans, and supplementation with a mixture of all L-amino acids only partially rescues fertility. In the present study, we demonstrate that dietary L-glutamate is the responsible amino acid that can increase fertility in hermaphrodite pept-1 worms. This effect was associated with a significantly higher uptake of glutamate/aspartate in pept-1 than in wildtype C. elegans. Furthermore, we found that the intestinal transporter proteins SNF-5 of the solute carrier SLC6 family of nutrient amino acid transporters (NAT) and AAT-6 of the SLC7 family as the light subunit of a heteromeric amino acid transporter (HAT) play a key role in glutamate homeostasis in pept-1 C. elegans. Genes encoding these transporters are highly expressed and upon silencing a 95% reduced fertility (snf-5) and sterility (aat-6) was observed. A subsequent L-glutamate supplementation failed to rescue these phenotypes. Dietary glutamate supplementation did neither influence the feeding frequency, nor did it improve mating efficiency of pept-1 males. Most strikingly, pept-1 were more prone to habituation to repeated gentle touch stimuli than wildtype C. elegans, and dietary glutamate supply was sufficient to alter this behavioral output by restoring the mechanosensory response to wildtype levels. Taken together, our data demonstrate a key role of L-glutamate in amino acid homeostasis in C. elegans lacking the peptide transporter in the intestine and demonstrate its distinct role in reproduction and for neural circuits mediating touch sensitivity.

Metabolomics has identified biomarkers in human plasma with a predictive quality for type 2 diabetes (T2D) development. Amongst these markers are various acylcarnitine species, most prominently those derived from branched-chain amino acid (BCAA) breakdown. The metabolic perturbations in tissues underlying these changes in plasma are often unknown and hard to assess in humans. Thus, animal models are used to have access to the different tissues. In contrast to diet-induced obesity models or monogenetic mouse models of obesity and diabetes, the New Zealand Obese (NZO) mouse is a prototypical polygenic model for obesity, with a male-specific susceptibility to developing diabetes. We have used this model to study the metabolic alterations in obesity-induced diabetes for changes in tissue-specific acylcarnitine and amino acid profiles. Twelve male and 11 female NZO mice at an age of 8 weeks were fed a chemically-defined high carbohydrate diet for 12 weeks. Acylcarnitine and amino acid profiles were obtained from plasma, skeletal muscle, heart muscle, liver, kidney and adipose tissues, using a high-resolution LC-MS/MS method. This method covered around 35 amino acids and 43 acylcarnitine species originating from fatty acids and amino acids, as well as odd-numbered and dicarboxylic acylcarnitines. Furthermore, blood glucose, plasma insulin, non-esterified fatty acids (NEFA), triglyceride and urea concentrations were measured. Hierarchical cluster analysis of principle components derived from plasma samples revealed a grouping of normoglycemic females, normoglycemic males and hyperglycemic males and this originated mainly from differences in concentrations of acylcarnitines derived from BCAAs and odd-numbered short- and medium-chain fatty acids. Hyperglycemic males were characterized by high insulin levels and low levels of NEFAs. These findings largely match with findings in humans. Comparison of metabolite profiles in diabetic and non-diabetic male mice revealed the largest overlap of significant metabolite changes between plasma and liver, including longer-chain odd-numbered acylcarnitine species. In conclusion, the alterations in acylcarnitine and amino acid profiles in NZO mice largely overlap with findings in humans, suggesting similar underlying metabolic perturbations in this diabetes model as compared to humans. The metabolite profiling of individual tissues in this model suggests a specific role of the liver in the generation of odd-numbered fatty acylcarnitines.

Enterohemorrhagic E. coli O157:H7 (EHEC) shorten the lifespan of Caenorhabditis elegans compared to avirulent bacteria. Co-feeding EHEC with Enterococcus faecalis Symbioflor® significantly increased the worms' lifespan. The transcriptome of EHEC grown in vitro with or without Symbioflor® was analyzed using RNA-seq. The analysis revealed downregulation of several virulence-associated genes in the presence of Symbioflor®, including virulence key genes (e.g., LEE, flagellum, quorum-sensing). The downregulation of the LEE genes was corroborated by lux-transposon mutants. Upregulated genes included acid response genes, due to a decrease in pH exerted by Symbioflor®. Further genes indicate cellular stress in EHEC (e.g. prophage/mobile elements involved in excision, cell lysis, and cell division inhibition). Thus, the observed protection of C. elegans during an EHEC infection by the probiotic Symbioflor® is suggested to be caused by triggering concomitant transcriptomic changes. To verify the biological relevance of this modulation, exemplary genes found to be influenced by Symbioflor® were knocked out (fliD, espB, Z3136, Z3917, and L7052). The lifespan of nematodes changed when using knock-outs as food source and the effect could be complemented in trans. In summary, Symbioflor® appears to be a protective probiotic in the nematode model.

BackgroundTrans‐resveratrol (RES) has received considerable interest in biomedical research in the last decade for its attributed health benefits and as a putative “energy restriction mimetic”. However, findings are mainly derived from model organisms including worms, fruit flies, and mice and usually do no take into account that biotransformation of RES may be species‐specific. Knowledge on the biotransformation processes may also explain better the inconsistency of biological data collected on RES.AimTo study the metabolism of RES in the different species in a comparative mannerMethodCaenorhabditis elegans (wild‐type N2, variety Bristol), grown for 48 h on NGM agar containing 100 μM RES and heat‐killed bacteria as food, were washed, homogenized and extracted with methanol. Fruit flies (Drosophila melanogaster) of the line w1118 (Bloomington Drosophila Stock Center, #5905) were raised on standard cornmeal‐agar medium supplemented with RES (200 and 500 μM). Flies were kept at a density of 50 animals per vial for at least one week. Male C57BL/6N mice (n=6) were fed a RES supplemented diet for 14 days, killed and blood was collected (German Animal Ethics Committee; ref. no: 55.2‐1‐54‐2532‐22‐11). 6 male healthy men ingested a single dose of a RES containing grapevine shoot extract (0.5 mg RES/mg KG). Blood and urine samples were collected (German Clinical Trials Register as DRKS00004311, Universal Trial Number (WHO) UTN: U1111‐1133–4621). All samples were analyzed under standardised conditions with LC‐DAD‐QToF‐MS/MS. Metabolites were characterized using fragmentation pattern, accurate masses and in part by reference substances.ResultsRES was extensively metabolized in C. elegans as well as in mice, but the metabolite profiles were highly diverse. In C. elegans at least 9 different sugar conjugates with RES‐phosphoglucoside and RES‐3‐glucoside as the predominant metabolites were found. In mice, at least 8 sulfate and glucuronide conjugates of RES and dihydro‐RES, a metabolite formed by the gut microbiota, were detected with dihydro‐RES‐glucuronide and ‐disulfate as the major entities. Only 18% of RES was found as the parent compound in worms and <1% in mice. In Drosophila, essentially the same phosphoglucoside and 3‐O‐glucoside conjugates were found like in C. elegans although the extent of conjugation appeared much lower with the RES aglycone dominating the spectrum. In humans, RES‐3‐sulfate was the main metabolite in plasma 1 h after ingestion whereas in the urine 12–24 h after ingestion dihydro‐RES and lunularin conjugates predominated but with huge interindividual variation.ConclusionSignificant differences in the biotransformation of RES between the species were observed. In mice and humans the metabolism of RES by the gut microflora is of major importance whereas these processes do not seem to play a role in worms and flies. Mice and humans differ regarding the phase‐II metabolism with huge interindividual differences in humans. Little is known about the biological activities of the various RES metabolites identified which warrants further investigations.

Acylcarnitines are intermediates of fatty acid and amino acid oxidation found in tissues and body fluids. They are important diagnostic markers for inherited diseases of peroxisomal and mitochondrial oxidation processes and were recently described as biomarkers of complex diseases like the metabolic syndrome. Quantification of acylcarnitine species can become challenging because various species occur as isomers and/or have very low concentrations. Here we describe a new LC-MS/MS method for quantification of 56 acylcarnitine species with acyl-chain lengths from C2 to C18. Our method includes amino acid-derived positional isomers, like methacrylyl-carnitine (2-M-C3:1-CN) and crotonyl-carnitine (C4:1-CN), and odd-numbered carbon species, like pentadecanoyl-carnitine (C15:0-CN) and heptadecanoyl-carnitine (C17:0-CN), occurring at very low concentrations in plasma and tissues. Method validation in plasma and liver samples showed high sensitivity and excellent accuracy and precision. In an application to samples from streptozotocin-treated diabetic mice, we identified significantly increased concentrations of acylcarnitines derived from branched-chain amino acid degradation and of odd-numbered straight-chain species, recently proposed as potential biomarkers for the metabolic syndrome. In conclusion, the LC-MS/MS method presented here allows robust quantification of isomeric acylcarnitine species and extends the palette of acylcarnitines with diagnostic potential derived from fatty acid and amino acid metabolism.

Aims/hypothesis Metabolomics approaches in humans have identified around 40 plasma metabolites associated with insulin resistance (IR) and type 2 diabetes, which often coincide with those for obesity. We aimed to separate diabetes-associated from obesity-associated metabolite alterations in plasma and study the impact of metabolically important tissues on plasma metabolite concentrations.Methods Two obese mouse models were studied; one exclusively with obesity (ob/ob) and another with type 2 diabetes (db/db). Both models have impaired leptin signalling as a cause for obesity, but the different genetic backgrounds determine the susceptibility to diabetes. In these mice, we profiled plasma, liver, skeletal muscle and adipose tissue via semi-quantitative GC-MS and quantitative liquid chromatography (LC)-MS/MS for a wide range of metabolites.Results Metabolite profiling identified 24 metabolites specifically associated with diabetes but not with obesity. Among these are known markers such as 1,5-anhydro-d-sorbitol, 3-hydroxybutyrate and the recently reported marker glyoxylate. New metabolites in the diabetic model were lysine, O-phosphotyrosine and branched-chain fatty acids. We also identified 33 metabolites that were similarly altered in both models, represented by branched-chain amino acids (BCAA) as well as glycine, serine, trans-4-hydroxyproline, and various lipid species and derivatives. Correlation analyses showed stronger associations for plasma amino acids with adipose tissue metabolites in db/db mice compared with ob/ob mice, suggesting a prominent contribution of adipose tissue to changes in plasma in a diabetic state.Conclusions/interpretation By studying mice with metabolite signatures that resemble obesity and diabetes in humans, we have found new metabolite entities for validation in appropriate human cohorts and revealed their possible tissue of origin.